Phenothiazine analogues as mitochondrial therapeutic agents

ABSTRACT

The present disclosure provides phenothiazine derivative compounds and salts thereof, compositions comprising these compounds, and methods of using these compounds in a variety of applications, such as treatment or suppression of diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of the filing dates of U.S. Provisional Patent Application Ser. No. 62/117,205, filed Feb. 17, 2015, which is hereby incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION Field of the Invention

The present disclosure provides phenothiazine derivative compounds and salts thereof, compositions comprising these compounds, and methods of using these compounds in a variety of applications, such as treatment or suppression of diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation.

Description of Related Art

Mitochondria are intracellular organelles responsible for a number of metabolic transformations and regulatory functions. They produce much of the ATP employed by eukaryotic cells. They are also the major source of free radicals and reactive oxygen species that cause oxidative stress. Consequently, mitochondrial defects are damaging, particularly to neural and muscle tissues which have high energy level demands. Thus, energetic defects have been implicated in forms of movement disorders, cardiomyopathy, myopathy, blindness, and deafness (DiMauro et al. (2001) Am. J. Med Genet. 106, 18-26; Leonard et al. (2000) Lancet. 355, 299-304). There are a number of mitochondrial diseases resulting from both nuclear and mitochondrial genetic defects, and the underlying biochemistries of these diseases tend to be rather similar. They include increased lactate production, diminished respiration and ATP production, and reflect the consequences of oxidative stress. Mitochondrial dysfunction is linked to numerous neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, Huntington's disease, and Friedreich's ataxia.

SUMMARY OF THE INVENTION

We recognized a need for therapies that target diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation. Thus, this disclosure is generally directed describes novel compounds for the treatment or suppression of such diseases. The inventors have found that the compounds of the disclosure confer cytoprotection and quenched ROS and lipid peroxidation in a dose-dependent manner in Friedreich's ataxia (FRDA) lymphocytes at low micromolar concentrations. The compounds of the disclosure also prevent ROS-induced damage of cellular lipid membranes and maintain the mitochondrial membrane potential of FRDA lymphocytes. In addition, the compounds of the disclosure significantly increased frataxin levels. The disclosure also describes use of these compounds for the treatment of mitochondrial disorders, including but not limited to Friedreich's ataxia, Leber's Hereditary Optic Neuropathy, Kearns-Sayre Syndrome, Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-Like Episodes and more generally, any disease associated with impairment of energy production and mitochondrial function. Aging may also involve decreased mitochondrial function and diminished ATP production, and the therapeutic agents described here may also find utility in mitigating the effects of aging.

Thus, in one aspect, the disclosure provides a compound of formula (I):

-   wherein -   Y is ═O or ═N⁺R⁴R⁵X⁻, where X⁻ is a counterion; -   R¹ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, —OR⁷,     —SR⁷, or —N(R⁷)₂, each optionally substituted with one to four     substituents selected from halogen, —CN, —NO₂, C₁-C₆ alkyl,     halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl,     C₃-C₈cycloalkenyl, aryl, heteroaryl, and heterocycle, wherein each     cycloalkyl, cycloalkenyl, aryl, heteroaryl, and heterocycle are     optionally substituted with one or more R⁹;     -   where each R⁷ independently is hydrogen, C₁-C₆ alkyl, or         halo(C₁-C₆ alkyl);     -   where each R⁸ independently is hydrogen, C₁-C₆ alkyl, halo(C₁-C₆         alkyl), C₃-C₈ cycloalkyl, aryl, heteroaryl, heterocycle,         aryl(C₁-C₆ alkyl), C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆         alkyl), heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆ alkyl),         wherein each cycloalkyl, aryl, heteroaryl, and heterocycle are         optionally substituted with one or more R⁹;     -   where each R⁹ independently is halogen, —CN, —NO₂, —N₃, C₁-C₆         alkyl, halo(C₁-C₆ alkyl), C₁-C₆ alkoxy, amino, C₁-C₆alkylamino,         or diC₁-C₆alkylamino; -   R² is —N(R¹²)₂, where R¹² groups together with the nitrogen to which     they are attached form a heterocycle optionally substituted with one     or more R⁹; -   R³ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, or     —OR⁷, each optionally substituted with one to four substituents     selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl),     —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl,     aryl, heteroaryl, and heterocycle, wherein each cycloalkyl,     cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally     substituted with R⁹; -   R⁴ and R⁵ together with nitrogen to which they are attached form a     heterocycle optionally substituted with one or more R⁹; -   each R⁶ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl,     C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, aryl, heteroaryl, heterocycle,     —OR¹⁰, or —N(R¹¹)₂, wherein each alkyl, alkenyl, and alkynyl are     optionally substituted with one to four substituents selected from     halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂,     —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl optionally substituted with R⁹,     C₃-C₈ cycloalkenyl optionally substituted with R⁹, aryl optionally     substituted with R⁹, heteroaryl optionally substituted with R⁹, and     heterocycle optionally substituted with R⁹; where R¹⁰ is C₁-C₆     alkyl, halo(C₁-C₆ alkyl), C₃-C₈ cycloalkyl, aryl, heteroaryl,     heterocycle, aryl(C₁-C₆ alkyl), C₃-C₈cycloalkyl(C₁-C₆ alkyl),     aryl(C₁-C₆ alkyl), heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆     alkyl), wherein each cycloalkyl, aryl, heteroaryl, and heterocycle     are optionally substituted with R⁹; and where each R¹¹ independently     is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl.

Another aspect of the disclosure provides a compound of formula (II):

-   wherein -   X⁻ is a counterion; -   R¹ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, —OR⁷,     —SR⁷, —NHR⁷, or —N(R⁷)₂, each optionally substituted with one to     four substituents selected from halogen, —CN, —NO₂, C₁-C₆ alkyl,     halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl,     C₃-C₈cycloalkenyl, aryl, heteroaryl, and heterocycle, wherein each     cycloalkyl, cycloalkenyl, aryl, heteroaryl, and heterocycle are     optionally substituted with one or more R⁹;     -   where each R⁷ independently is hydrogen, C₁-C₆ alkyl, or         halo(C₁-C₆ alkyl);     -   where each R⁸ independently is hydrogen, C₁-C₆ alkyl, halo(C₁-C₆         alkyl), C₃-C₈ cycloalkyl, aryl, heteroaryl, heterocycle,         aryl(C₁-C₆ alkyl), C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆         alkyl), heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆ alkyl),         wherein each cycloalkyl, aryl, heteroaryl, and heterocycle are         optionally substituted with one or more R⁹;     -   where each R⁹ independently is halogen, —CN, —NO₂, —N₃, C₁-C₆         alkyl, halo(C₁-C₆ alkyl), C₁-C₆ alkoxy, amino, C₁-C₆alkylamino,         or diC₁-C₆alkylamino; -   R² and R⁶ are independently —N(R¹¹)₂;     -   where each R¹¹ independently is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀         alkenyl, or C₂-C₂₀ alkynyl; -   R³ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, or     —OR⁷, each optionally substituted with one to four substituents     selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl),     —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl,     aryl, heteroaryl, and heterocycle, wherein each cycloalkyl,     cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally     substituted with R⁹; -   R⁴ and R⁵ are independently C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀     alkynyl, each optionally substituted with one to four substituents     selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl),     —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl,     aryl, heteroaryl, and heterocycle, wherein each cycloalkyl,     cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally     substituted with R⁹;     -   where R¹⁰ is C₁-C₆ alkyl, halo(C₁-C₆ alkyl), C₃-C₈ cycloalkyl,         aryl, heteroaryl, heterocycle, aryl(C₁-C₆ alkyl),         C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆ alkyl),         heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆ alkyl), wherein         each cycloalkyl, aryl, heteroaryl, and heterocycle are         optionally substituted with R⁹; and -   R⁷ is hydrogen or —N(R¹¹)₂.

Another aspect of the disclosure provides pharmaceutical compositions comprising the compounds and salts of the disclosure and an appropriate carrier, excipient or diluent. The exact nature of the carrier, excipient or diluent will depend upon the desired use for the composition, and may range from being suitable for veterinary uses to being suitable for human use. The compositions may optionally include one or more additional compounds suitable for a use.

Another aspect of the disclosure provides methods of treating or suppressing diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation, comprising administering an effective amount of the compound and salts of the disclosure.

Another aspect of the disclosure provides a method of treating or suppressing one or more of Friedreich's ataxia, Leber's Hereditary Optic Neuropathy, Kearns-Sayre Syndrome, Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-Like Episodes, or Leigh syndrome, comprising administering an effective amount of the compound and salts of the disclosure.

Another aspect of the disclosure provides a method of treating or suppressing one or more of obesity, atherosclerosis, amyotrophic lateral sclerosis, Parkinson's Disease, cancer, heart failure, myocardial infarction (MI), Alzheimer's Disease, Huntington's Disease, schizophrenia, bipolar disorder, fragile X syndrome, chronic fatigue syndrome, and Leigh syndrome, comprising administering an effective amount of the compound and salts of the disclosure.

DESCRIPTION OF DRAWINGS

The results set forth herein, and the properties and characteristics of the compounds provided by the disclosure, can be advantageously understood with regard to the drawings.

FIG. 1 shows the results of effect of the compounds of the disclosure on cytotoxicity. Cultured FRDA lymphocytes were incubated for 24 h or 48 h in glucose free media (galactose) to force cells to rely on mitochondria to produce their ATP. Flow cytometric determination of cell viability by fluorescence labeling was used employing calcein acetoxy-methyl-ester and ethidium homodimer-1 as live and dead cell stains. MB is methylene blue (3,7-bis(dimethylamino)phenazathionium chloride); MV is methylene violet (7-(dimethylamino)-3H-phenothiazin-3-one).

FIG. 2 shows flow cytometric analysis of FRDA lymphocyte cells stained with dichlorodihydrofluorescein diacetate (DCFH-DA) for 20 min, following pretreatment with the test compounds for 16 h, and subsequent treatment with diethyl maleate (DEM) for 80 min to induce the production of reactive oxygen species (ROS) by depleting glutathione level.

FIG. 3 shows flow cytometric analysis shows the effect of test compounds on Δψ_(m) in FRDA lymphocyte cells using the ratiometric fluorescent probe JC-1. This probe is a cell penetrating dye that accumulates within mitochondria maintaining high Δψ_(m). Dark gray regions represent intact mitochondrial membranes with JC-1 aggregates (red fluorescence), whereas the gated region in light gray depicts cells with loss of Δψ_(m). The bar graph shows the percentage of cells with intact Δψ_(m) calculated using Accuri™ C6 software. In each analysis, 10000 events were recorded. Depolarization with carbonyl cyanide p-(trifluoromethoxy)phenylhydrazone (FCCP), was used to serve as a positive control.

FIG. 4 shows total ATP level in FRDA lymphocytes following incubation with test compounds for 24 h in glucose free media (25 mM galactose). Results are expressed as percentage of total ATP relative to untreated control.

FIG. 5 illustrates cytoprotective effect of the test compounds in FRDA lymphocytes following preincubation with test compounds for 4 h in glucose free media and subsequent treatment with rotenone (50 nM) for 24 h or 48 h to inhibit complex I. Cell viability was measured by flow cytometry using fluorescence labeling with calcein acetoxy-methyl-ester and ethidium homodimer-1 as live and dead cell stains, respectively. Results are expressed as percentage live cells relative to untreated control

FIG. 6 shows the effect of compound 5 on bovine heart mitochondrial NADH oxidase activity (complexes I, III and IV) (NADH oxidase). Compound 5 was able redirect electron flow in the respiratory chain as a result of NADH oxidation even in complex I completely blocked by rotenone.

FIG. 7 shows bovine heart mitochondrial complex I (SMP) activity in presence of a number of the test compounds.

FIG. 8 illustrates in vitro SIRT3 deacetylation activity, complex I activity in bovine heart submitochondrial particles (SMP) was coupled with recombinant SIRT3 (rSIRT3) activity using a luminogenic acetylated SIRT3 peptide substrate. The co-substrate NAD⁺ was generated from oxidation of NADH by complex I in presence and absence of rotenone.

FIG. 9 illustrates western blot showing the effect of MB and its analogue compound 33 on the level of frataxin in FRDA lymphocytes. Methylene blue slightly increased frataxin at lower concentration but did not at higher concentration. The modified analogue compound 33 significantly increased frataxin levels at both concentrations.

DETAILED DESCRIPTION OF THE INVENTION

Before the disclosed methods are described, it is to be understood that the aspects described herein are not limited to specific embodiments, or compositions, and as such can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and, unless specifically defined herein, is not intended to be limiting.

Throughout this specification, unless the context requires otherwise, the word “comprise” and “include” and variations (e.g., “comprises,” “comprising,” “includes,” “including”) will be understood to imply the inclusion of a stated component, feature, element, or step or group of components, features, elements or steps but not the exclusion of any other integer or step or group of integers or steps.

As used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.

In view of the present disclosure, the compositions and methods described herein can be configured by the person of ordinary skill in the art to meet the desired need. In general, the disclosed compounds and methods provide improvements in the treatment of diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation. For example, in particular embodiments, the compounds of the disclosure confer cytoprotection and quenched ROS and lipid peroxidation in a dose-dependent manner in Friedreich's ataxia (FRDA) lymphocytes at low micromolar concentrations. The compounds of the disclosure also prevent ROS-induced damage of cellular lipid membranes and maintain the mitochondrial membrane potential of FRDA lymphocytes. The compounds of the disclosure (for example, compound 33) also significantly increased frataxin levels.

In one aspect, the disclosure provides a compound of formula (I):

-   wherein -   Y is ═O or ═N⁺R⁴R⁵X⁻, where X⁻ is a counterion; -   R¹ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, —OR⁷,     —SR⁷, or —N(R⁷)₂, each optionally substituted with one to four     substituents selected from halogen, —CN, —NO₂, C₁-C₆ alkyl,     halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl,     C₃-C₈cycloalkenyl, aryl, heteroaryl, and heterocycle, wherein each     cycloalkyl, cycloalkenyl, aryl, heteroaryl, and heterocycle are     optionally substituted with one or more R⁹;     -   where each R⁷ independently is hydrogen, C₁-C₆ alkyl, or         halo(C₁-C₆ alkyl);     -   where each R⁸ independently is hydrogen, C₁-C₆ alkyl, halo(C₁-C₆         alkyl), C₃-C₈ cycloalkyl, aryl, heteroaryl, heterocycle,         aryl(C₁-C₆ alkyl), C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆         alkyl), heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆ alkyl),         wherein each cycloalkyl, aryl, heteroaryl, and heterocycle are         optionally substituted with one or more R⁹;     -   where each R⁹ independently is halogen, —CN, —NO₂, —N₃, C₁-C₆         alkyl, halo(C₁-C₆ alkyl), C₁-C₆ alkoxy, amino, C₁-C₆alkylamino,         or diC₁-C₆alkylamino; -   R² is —N(R¹²)₂, where R¹² groups together with the nitrogen to which     they are attached form a heterocycle optionally substituted with one     or more R⁹; -   R³ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, or     —OR⁷, each optionally substituted with one to four substituents     selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl),     —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl,     aryl, heteroaryl, and heterocycle, wherein each cycloalkyl,     cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally     substituted with R⁹; -   R⁴ and R⁵ together with nitrogen to which they are attached form a     heterocycle optionally substituted with one or more R⁹; -   each R⁶ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl,     C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, aryl, heteroaryl, heterocycle,     —OR¹⁰, or —N(R¹¹)₂, wherein each alkyl, alkenyl, and alkynyl are     optionally substituted with one to four substituents selected from     halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂,     —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl optionally substituted with R⁹,     C₃-C₈ cycloalkenyl optionally substituted with R⁹, aryl optionally     substituted with R⁹, heteroaryl optionally substituted with R⁹, and     heterocycle optionally substituted with R⁹;     -   where R¹⁰ is C₁-C₆ alkyl, halo(C₁-C₆ alkyl), C₃-C₈ cycloalkyl,         aryl, heteroaryl, heterocycle, aryl(C₁-C₆ alkyl),         C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆ alkyl),         heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆ alkyl), wherein         each cycloalkyl, aryl, heteroaryl, and heterocycle are         optionally substituted with R⁹; and     -   where each R¹¹ independently is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀         alkenyl, or C₂-C₂₀ alkynyl.

In one embodiment, the disclosure provides compounds of formula (I), wherein R¹ is hydrogen, optionally substituted alkyl, optionally substituted C₂-C₂₀ alkenyl, optionally substituted C₂-C₂₀ alkynyl, or —OR⁷. In some embodiments, R¹ is hydrogen. In some other embodiments, R¹ is optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In some embodiments, R¹ is alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), wherein the alkyl is optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In one embodiment, R¹ is C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), wherein the alkyl is optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In another embodiment, R¹ is —OR⁷ and R⁷ is C₁-C₆ alkyl.

In another embodiment, the disclosure provides compounds of formula (I), wherein R² is piperazinyl, piperidinyl, morpholinyl, pyrrolidinyl, azepanyl, or diazepanyl, each optionally substituted with one or more R⁹. In one embodiment, R² is piperidinyl optionally substituted with one or more R⁹. In another embodiment, R² is unsubstituted piperidinyl. In one embodiment, R² is morpholinyl optionally substituted with one or more R⁹. In another embodiment, R² is unsubstituted morpholinyl.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (I), wherein R³ is hydrogen, optionally substituted C₁-C₂₀ alkyl, or —OR⁷. In another embodiment, R³ is hydrogen.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (I), wherein R³ is optionally substituted C₁-C₂₀ alkyl. In one embodiment, R³ is C₁-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In another embodiment, R³ is C₁-C₂₀ alkyl optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In yet another embodiment, R³ is unsubstituted C₁-C₂₀ alkyl.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (I), wherein R³ is optionally substituted C₃-C₂₀ alkyl, or R³ is optionally substituted C₄-C₂₀ alkyl, or R³ is optionally substituted C₅-C₂₀ alkyl. In one embodiment, R³ is C₅-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In another embodiment, R³ is C₅-C₂₀ alkyl optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In one embodiment, R³ is unsubstituted C₃-C₂₀ alkyl, or R³ is unsubstituted C₄-C₂₀ alkyl, or R³ is unsubstituted C₅-C₂₀ alkyl.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (I), wherein R³ is optionally substituted C₆-C₂₀ alkyl, or R³ is optionally substituted C₇-C₂₀ alkyl, or R³ is optionally substituted C₈-C₂₀ alkyl. In one embodiment, R³ is C₇-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In another embodiment, R³ is C₇-C₂₀ alkyl optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In yet another embodiment, R³ is unsubstituted C₆-C₂₀ alkyl, R³ is unsubstituted C₇-C₂₀ alkyl, or R³ is unsubstituted C₈-C₂₀ alkyl.

In one embodiment, the compounds of formula (I) are those wherein R³ is C₁₀-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In one embodiment, R³ is C₁₀-C₂₀ alkyl optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In another embodiment, R³ is unsubstituted C₁₀-C₂₀ alkyl. In yet another embodiment, R³ is heptadecyl.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (I), wherein R³ is —OR⁷ and R⁷ is C₁-C₆ alkyl.

In another embodiment, the disclosure provides compounds as described above with any reference to formula (I), wherein Y is ═O.

In another embodiment, the disclosure provides compounds as described above with any reference to formula (I), wherein Y is ═N⁺R⁴R⁵X⁻. In one embodiment, X⁻ is a counterion. Counterions may include inorganic or organic counterions. Inorganic counterions include, by way of example and not limitation, halide (e.g., chloride, bromide, iodide, etc.), sulfate, nitrate, phosphate, hydroxide, oxide, and the like. Organic counterions include, by way of example and not limitation, acetate, monofluoroacetate, difluoroacetate, trifluoroacetate, propionate, hexanoate, cyclopentanepropionate, glycolate, oxalate, pyruvate, lactate, malonate, succinate, malate, maleate, fumarate, tartarate, citrate, palmitate, benzoate, 3-(4-hydroxybenzoyl)benzoate, cinnamate, mandelate, alkyl sulfonates (e.g., methanesulfonate, ethanesulfonate, 1,2-ethane-disulfonate, 2-hydroxyethanesulfonate, etc.), aryl sulfonates (e.g., benzenesulfonate, 4-chlorobenzenesulfonate, 2-naphthalenesulfonate, 4-toluenesulfonate, camphorsulfonate, etc.), 4-methylbicyclo[2.2.2]-oct-2-ene-1-carboxylate, glucoheptonate, 3-phenylpropionate, trimethylacetate, tertiary butylacetate, lauryl sulfurate, gluconate, glutamate, hydroxynaphthoate, salicylate, stearate, muconate, and the like. In one embodiment, X⁻ is halogen. In another embodiment, X⁻ is I⁻.

In one embodiment, the compounds of formula (I) are those wherein R⁴ is optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In another embodiment, R⁴ is C₁-C₆ alkyl.

In one embodiment, the compounds of formula (I) are those wherein R⁵ is optionally substituted C₁-C₂₀ alkyl(or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In another embodiment, R⁵ is C₁-C₆ alkyl.

In one embodiment, the disclosure provides compounds of formula (I), wherein R⁴ and R⁵ together with nitrogen to which they are attached form piperazinyl, piperidinyl, morpholinyl, pyrrolidinyl, azepanyl, or diazepanyl, each optionally substituted with one or more R⁹. In another embodiment, R⁴ and R⁵ together with nitrogen to which they are attached form piperidinyl optionally substituted with one or more R⁹. In yet another embodiment, R⁴ and R⁵ together with nitrogen to which they are attached form unsubstituted piperidinyl. In some embodiments, R⁴ and R⁵ together with nitrogen to which they are attached form morpholinyl optionally substituted with one or more R⁹. In some other embodiments, R⁴ and R⁵ together with nitrogen to which they are attached form unsubstituted morpholinyl.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (I), wherein R⁶ is hydrogen, optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), or —N(R¹¹)₂. In another embodiment, R⁶ is hydrogen or optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In some embodiments, R⁶ is hydrogen.

In some other embodiments, R⁶ is alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), wherein the alkyl is optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹.

In some other embodiments, R⁶ is C₁-C₂₀ alkyl (or C₁-C₂₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), wherein the alkyl is optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹.

In one embodiment, the compounds of formula (I) are those wherein R⁶ is —N(R¹¹)₂.

In one embodiment, each R¹¹ is independently hydrogen or C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In another embodiment, each R¹¹ is independently hydrogen or C₁-C₆ alkyl. In another embodiment, each R¹¹ is independently C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl. In another embodiment, each R¹¹ is independently methyl or ethyl. In another embodiment, each R¹¹ is independently methyl.

In another embodiment, the compounds of formula (I) are those wherein R⁶ is —OR¹⁰, where R¹⁰ is C₁-C₆ alkyl optionally substituted with R⁹. In another embodiment, R⁶ is —OR¹⁰, where R¹⁰ is aryl or aryl(C₁-C₆ alkyl), where each aryl is optionally substituted with R⁹.

Exemplary compounds of formula (I) include:

In one aspect, the disclosure provides a compound of formula (II):

-   wherein -   X⁻ is a counterion; -   R¹ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, —OR⁷,     —SR⁷, —NHR⁷, or —N(R⁷)₂, each optionally substituted with one to     four substituents selected from halogen, —CN, —NO₂, C₁-C₆ alkyl,     halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl,     C₃-C₈cycloalkenyl, aryl, heteroaryl, and heterocycle, wherein each     cycloalkyl, cycloalkenyl, aryl, heteroaryl, and heterocycle are     optionally substituted with one or more R⁹;     -   where each R⁷ independently is hydrogen, C₁-C₆ alkyl, or         halo(C₁-C₆ alkyl);     -   where each R⁸ independently is hydrogen, C₁-C₆ alkyl, halo(C₁-C₆         alkyl), C₃-C₈ cycloalkyl, aryl, heteroaryl, heterocycle,         aryl(C₁-C₆ alkyl), C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆         alkyl), heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆ alkyl),         wherein each cycloalkyl, aryl, heteroaryl, and heterocycle are         optionally substituted with one or more R⁹;     -   where each R⁹ independently is halogen, —CN, —NO₂, —N₃, C₁-C₆         alkyl, halo(C₁-C₆ alkyl), C₁-C₆ alkoxy, amino, C₁-C₆alkylamino,         or diC₁-C₆alkylamino; -   R² and R⁶ are independently —N(R¹¹)₂;     -   where each R¹¹ independently is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀         alkenyl, or C₂-C₂₀ alkynyl; -   R³ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, or     —OR⁷, each optionally substituted with one to four substituents     selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl),     —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl,     aryl, heteroaryl, and heterocycle, wherein each cycloalkyl,     cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally     substituted with R⁹; -   R⁴ and R⁵ are independently C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀     alkynyl, each optionally substituted with one to four substituents     selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl),     —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl,     aryl, heteroaryl, and heterocycle, wherein each cycloalkyl,     cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally     substituted with R⁹; where R¹⁰ is C₁-C₆ alkyl, halo(C₁-C₆ alkyl),     C₃-C₈ cycloalkyl, aryl, heteroaryl, heterocycle, aryl(C₁-C₆ alkyl),     C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆ alkyl), heteroaryl(C₁-C₆     alkyl), or heterocycle(C₁-C₆ alkyl), wherein each cycloalkyl, aryl,     heteroaryl, and heterocycle are optionally substituted with R⁹; and -   R⁷ is hydrogen or —N(R¹¹)₂.

In one embodiment, the disclosure provides compounds of formula (II), wherein R¹ is hydrogen, optionally substituted C₁-C₂₀ alkyl, optionally substituted C₂-C₂₀ alkenyl, optionally substituted C₂-C₂₀ alkynyl, or —OR⁷. In some embodiments, R¹ is hydrogen. In some other embodiments, R¹ is optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In some embodiments, R¹ is C₁-C₆ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), wherein the alkyl is optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In other embodiments, R¹ is C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), wherein the alkyl is optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In other embodiments, R¹ is —OR⁷ and R⁷ is C₁-C₆ alkyl.

In another embodiment, the disclosure provides compounds of formula (II), wherein R² is —N(R¹¹)₂, where each R¹¹ independently is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl. In one embodiment, R² is —N(R¹¹)₂, where each R¹¹ independently is C₁-C₆ alkyl, C₂-C₆ alkenyl, or C₂-C₆ alkynyl.

In one embodiment, the disclosure provides compounds of formula (II), wherein R² is —N(R^(u))₂, where each R¹¹ independently is C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In some embodiments, each R¹¹ independently is C₁-C₆ alkyl. In another embodiment, each R¹¹ is independently C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl. In another embodiment, each R¹¹ is independently methyl or ethyl. In another embodiment, each R¹¹ is independently methyl. For example, in some embodiments, R² is —N(CH₃)₂.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R³ is hydrogen, optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), or —OR⁷.

In another embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R³ is hydrogen. In yet another embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R³ is optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In one embodiment, the compounds of formula (II) are those wherein R³ is C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), wherein the alkyl is optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In another embodiment, the compounds of formula (II) are those wherein R³ is C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl), wherein the alkyl is optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In yet another embodiment, R³ is unsubstituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl).

In some embodiments of formula (II), R³ is C₅-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In some other embodiments, R³ is C₅-C₂₀ alkyl optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In some embodiments, R³ is unsubstituted C₅-C₂₀ alkyl.

In some embodiments of formula (II), R³ is C₇-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In some other embodiments of formula (II), R³ is C₇-C₂₀ alkyl optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In some embodiments, R³ is unsubstituted C₇-C₂₀ alkyl.

In some embodiments of formula (II), R³ is C₁₀-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In some other embodiments of formula (II), R³ is C₁₀-C₂₀ alkyl optionally substituted with C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹. In some embodiments, R³ is unsubstituted C₁₀-C₂₀ alkyl. For example, in some embodiments, R³ is heptadecyl.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R³ is —OR⁷ and R⁷ is C₁-C₆ alkyl.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R⁶ is —N(R¹¹)₂, and each R¹¹ is independently hydrogen or C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In one embodiment, each R¹¹ is independently C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In another embodiment, each R¹¹ is independently C₁-C₆ alkyl. In another embodiment, each R¹¹ is independently C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl. In another embodiment, each R¹¹ is independently methyl or ethyl. In another embodiment, each R¹¹ is independently methyl. For example, in certain embodiments, R⁶ is —N(CH₃)₂.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R⁴ is optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In one embodiment, R⁴ is unsubstituted C_(r) C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In certain embodiments, R⁴ is optionally substituted C₁-C₆ alkyl. In some other embodiments, R⁴ is unsubstituted C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl. In other embodiments, R⁴ is methyl.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R⁵ is optionally substituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In one embodiment, R⁵ is unsubstituted C₁-C₂₀ alkyl (or C₁-C₁₀ alkyl, or C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl, or C₂-C₂₀ alkyl, or C₃-C₂₀ alkyl, or C₄-C₂₀ alkyl, or C₆-C₂₀ alkyl, or C₈-C₂₀ alkyl). In certain embodiments, R⁵ is optionally substituted C₁-C₆ alkyl. In some other embodiments, R⁵ is unsubstituted C₁-C₆ alkyl, or C₁-C₄ alkyl, or C₁-C₃ alkyl. In other embodiments, R⁵ is methyl.

In one embodiment, the compounds of formula (II) are wherein X⁻ is a counterion. Counterions may include inorganic or organic counterions. Inorganic counterions include, by way of example and not limitation, halide (e.g., chloride, bromide, iodide, etc.), sulfate, nitrate, phosphate, hydroxide, oxide, and the like. Organic counterions include, by way of example and not limitation, acetate, monofluoroacetate, difluoroacetate, trifluoroacetate, propionate, hexanoate, cyclopentanepropionate, glycolate, oxalate, pyruvate, lactate, malonate, succinate, malate, maleate, fumarate, tartarate, citrate, palmitate, benzoate, 3-(4-hydroxybenzoyl)benzoate, cinnamate, mandelate, alkyl sulfonates (e.g., methanesulfonate, ethanesulfonate, 1,2-ethane-disulfonate, 2-hydroxyethanesulfonate, etc.), aryl sulfonates (e.g., benzenesulfonate, 4-chlorobenzenesulfonate, 2-naphthalenesulfonate, 4-toluenesulfonate, camphorsulfonate, etc.), 4-methylbicyclo[2.2.2]-oct-2-ene-1-carboxylate, glucoheptonate, 3-phenylpropionate, trimethylacetate, tertiary butylacetate, lauryl sulfurate, gluconate, glutamate, hydroxynaphthoate, salicylate, stearate, muconate, and the like.

In one embodiment, the compounds of formula (II) are wherein X⁻ is halogen. In another embodiment, X⁻ is I⁻.

In one embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R⁷ is hydrogen.

In another embodiment, the disclosure provides compounds as described above with any reference to formula (II), wherein R⁷ is —N(CH₃)₂.

Exemplary compounds of formula (II) include:

Another aspect of the disclosure provides a compound that is:

Therapeutic Applications

In one aspect, the disclosure provides a method for treating or protecting mitochondria with respiratory chain lesions, comprising administering to a subject in need of such treatment an effective amount of one or more compounds of the disclosure.

Compounds of the disclosure are useful, for example, for treating or suppressing diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation in a subject in need of treatment.

The present disclosure provides methods of treating conditions including but not limited to Friedreich's ataxia, Leber's Hereditary Optic Neuropathy, Kearns-Sayre Syndrome, Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-Like Episodes, and Leigh syndrome in a subject by administering an effective amount of a compound of the disclosure.

The disclosure also provides methods of treating conditions including but not limited to obesity, atherosclerosis, amyotrophic lateral sclerosis, Parkinson's Disease, cancer, heart failure, myocardial infarction (MI), Alzheimer's Disease, Huntington's Disease, schizophrenia, bipolar disorder, fragile X syndrome, chronic fatigue syndrome, and Leigh syndrome, in a subject by administering an effective amount of a compound of the disclosure.

In addition, the compounds of the disclosure can be used for prophylaxis of redox stress and enhancement of cellular function.

Friedreich's Ataxia

Friedreich's ataxia is a severe neurodegenerative and cardiodegenerative condition. It is characterized by progressive ataxia of the limbs, muscle weakness, dysarthria, skeletal deformities and cardiomyopathy. While the biochemical basis of the disease is still under investigation, it is strongly associated with insufficient frataxin (Wilson et al. (1997) Nat. Genet. 16, 352-357; Wilson et al. (2003) J. Neurol. Sci. 207, 103-105). In the majority of patients the insufficiency of frataxin is a consequence of an intronic GAA triplet repeat expansion in the gene for frataxin, which results in a significant decrease in its mRNA levels, and ultimately in protein levels as well (Campuzano et al. (1996) Science 271, 1423-1427; Campuzano et al. (1997) Hum. Mol. Genet. 6, 1771-1780). Frataxin acts as an iron chaperone during heme biosynthesis (Bencze et al. (2007) J.C.S. Chem. Commun. 1798-1800) and has been shown to be capable of stimulating the in vitro assembly of heme and Fe—S clusters (Park et al. (2003) J. Biol. Chem. 278, 31340-31351; Yoon et al. (2003) J. Am Chem. Soc. 125, 6078-6084; Yoon et al. (2004) J. Biol. Chem. 279, 25943-25946). Frataxin can interact physically with mitochondrial electron transport chain proteins, as well as with mitochondrial aconitase (which contains an Fe—S cluster) (Bulteau et al. (2004) Science 305, 242-245; Gonzalez-Cabo et al. (2005) Hum. Mol. Genet. 14, 2091-2098). Therefore, frataxin deficiency results in disruption of cellular iron homeostasis, with a progressive iron accumulation in the mitochondrion, and a deficiency in heme and Fe—S clusters.

It is believed that a deficiency in frataxin leads to compromised mitochondrial respiratory chain function through a failure to assemble one or more Fe-utilizing proteins; one or more Fe—S clusters in the mitochondrial respiratory complexes are likely to represent a critical locus. In fact, diminished function of these complexes has been noted in Friedreich's ataxia patients (Bradley et al. (2000) Hum. Mol. Genet. 9, 275-282). The loss of mitochondrial respiratory chain function can lead to diminished ATP production, while the accumulation of Fe in the mitochondria makes the organelle highly susceptible to oxidative damage by reactive oxygen species, whose concentration increases concomitant with the decrease in respiratory chain function. There is compelling evidence that while oxidative damage is not the primary lesion in Friedreich's ataxia, oxidative stress helps to drive disease progression. Therefore, strategies to overcome oxidative stress should blunt disease progression and provide effective therapy.

Other Exemplary Mitochondrial Diseases

Leber hereditary optic neuropathy is associated with degeneration of retinal ganglion cells and causes progressive loss of vision resulting in various degrees of blindness. Leber hereditary optic neuropathy primarily affects men over the age of 20 and is maternally transmitted due to mutations in the mitochondrial (not nuclear) genome.

Kearns-Sayre syndrome is a rare neuromuscular disorder typically with onset usually before the age of 20. It is characterized by progressive external ophthalmoplegia (paralysis of the eye muscles) and mild skeletal muscle weakness, hearing loss, loss of coordination, heart problems, and cognitive delays. There are many other names for the Kearns-Sayre syndrome including: Chronic progressive external ophthalmoplegia CPEO with myopathy; CPEO with ragged-red fibers; KSS; Mitochondrial cytopathy, Kearns-Sayre type; Oculocraniosomatic syndrome; Ophthalmoplegia-plus syndrome; Ophthalmoplegia with myopathy; and Ophthalmoplegia with ragged-red fibers.

Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-Like Episodes is a progressive mitochondrial disease that involves multiple organ systems including the central nervous system, cardiac muscle, skeletal muscle, and gastrointestinal system. Symptoms include muscle weakness, stroke-like events, eye muscle paralysis, and cognitive impairment. Leigh syndrome is a degenerative brain disorder is usually diagnosed at a young age (e.g. before age two). Deterioration is often rapid with symptoms such as seizures, dementia, feeding and speech difficulties, respiratory dysfunction, heart problems, and muscle weakness. Prognosis is poor with death typically occurring within a few years of diagnosis.

Pharmaceutical Compositions

In another aspect, the present disclosure provides pharmaceutical compositions comprising one or more of compounds of the disclosure. The term “pharmaceutical composition” is used in its widest sense, encompassing all pharmaceutically applicable compositions containing at least one active substance, and optional carriers, excipient, diluent, adjuvants, constituents etc. The term “pharmaceutical composition” also encompasses a composition comprising the active substance in the form of derivative or pro-drug, such as pharmaceutically acceptable salts and esters. The manufacture of pharmaceutical compositions for different routes of administration falls within the capabilities of a person skilled in medicinal chemistry. The exact nature of the carrier, excipient or diluent will depend upon the desired use for the composition, and may range from being suitable or acceptable for veterinary uses to being suitable or acceptable for human use. The composition may optionally include one or more additional compounds.

When used to treat or prevent such diseases, the compounds described herein may be administered singly, as mixtures of one or more compounds or in mixture or combination with other agents useful for treating such diseases and/or the symptoms associated with such diseases. The compounds may also be administered in mixture or in combination with agents useful to treat other disorders or maladies, such as steroids, membrane stabilizers, 5LO inhibitors, leukotriene synthesis and receptor inhibitors, inhibitors of IgE isotype switching or IgE synthesis, IgG isotype switching or IgG synthesis, β-agonists, tryptase inhibitors, aspirin, COX inhibitors, methotrexate, anti-TNF drugs, retuxin, PD4 inhibitors, p38 inhibitors, PDE4 inhibitors, and antihistamines, to name a few. The compounds may be administered in the form of compounds per se, or as pharmaceutical compositions comprising a compound.

Pharmaceutical compositions comprising the compound(s) may be manufactured by means of conventional mixing, dissolving, granulating, dragee-making levigating, emulsifying, encapsulating, entrapping or lyophilization processes. The compositions may be formulated in conventional manner using one or more physiologically acceptable carriers, diluents, excipients or auxiliaries which facilitate processing of the compounds into preparations which can be used pharmaceutically.

The compounds may be formulated in the pharmaceutical composition per se, or in the form of a hydrate, solvate, N-oxide or pharmaceutically acceptable salt, as previously described. Typically, such salts are more soluble in aqueous solutions than the corresponding free acids and bases, but salts having lower solubility than the corresponding free acids and bases may also be formed.

Pharmaceutical compositions may take a form suitable for virtually any mode of administration, including, for example, topical, ocular, oral, buccal, systemic, nasal, injection, transdermal, rectal, vaginal, etc., or a form suitable for administration by inhalation or insufflation.

For topical administration, the compound(s) may be formulated as solutions, gels, ointments, creams, suspensions, etc. as are well-known in the art. Systemic formulations include those designed for administration by injection, e.g., subcutaneous, intravenous, intramuscular, intrathecal or intraperitoneal injection, as well as those designed for transdermal, transmucosal oral or pulmonary administration.

Useful injectable preparations include sterile suspensions, solutions or emulsions of the active compound(s) in aqueous or oily vehicles. The compositions may also contain formulating agents, such as suspending, stabilizing and/or dispersing agent. The formulations for injection may be presented in unit dosage form, e.g., in ampules or in multidose containers, and may contain added preservatives. Alternatively, the injectable formulation may be provided in powder form for reconstitution with a suitable vehicle, including but not limited to sterile pyrogen free water, buffer, dextrose solution, etc., before use. To this end, the active compound(s) may be dried by any art-known technique, such as lyophilization, and reconstituted prior to use.

For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are known in the art.

For oral administration, the pharmaceutical compositions may take the form of, for example, lozenges, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinyl-pyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulfate). The tablets may be coated by methods well known in the art with, for example, sugars, films or enteric coatings.

Liquid preparations for oral administration may take the form of, for example, elixirs, solutions, syrups or suspensions, or they may be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, ethyl alcohol, Cremophore™ or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The preparations may also contain buffer salts, preservatives, flavoring, coloring and sweetening agents as appropriate.

Preparations for oral administration may be suitably formulated to give controlled release of the compound, as is well known.

For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.

For rectal and vaginal routes of administration, the compound(s) may be formulated as solutions (for retention enemas) suppositories or ointments containing conventional suppository bases such as cocoa butter or other glycerides.

For nasal administration or administration by inhalation or insufflation, the compound(s) can be conveniently delivered in the form of an aerosol spray from pressurized packs or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoro-methane, dichlorotetrafluoroethane, fluorocarbons, carbon dioxide or other suitable gas. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges for use in an inhaler or insufflator (for example capsules and cartridges comprised of gelatin) may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

For ocular administration, the compound(s) may be formulated as a solution, emulsion, suspension, etc. suitable for administration to the eye. A variety of vehicles suitable for administering compounds to the eye are known in the art.

For prolonged delivery, the compound(s) can be formulated as a depot preparation for administration by implantation or intramuscular injection. The compound(s) may be formulated with suitable polymeric or hydrophobic materials (e.g., as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, e.g., as a sparingly soluble salt. Alternatively, transdermal delivery systems manufactured as an adhesive disc or patch which slowly releases the compound(s) for percutaneous absorption may be used. To this end, permeation enhancers may be used to facilitate transdermal penetration of the compound(s).

Alternatively, other pharmaceutical delivery systems may be employed. Liposomes and emulsions are well-known examples of delivery vehicles that may be used to deliver compound(s). Certain organic solvents such as dimethylsulfoxide (DMSO) may also be employed, although usually at the cost of greater toxicity.

The pharmaceutical compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the compound(s). The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration.

The compound(s) described herein, or compositions thereof, will generally be used in an amount effective to achieve the intended result, for example in an amount effective to treat or prevent the particular disease being treated. By therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated and/or eradication or amelioration of one or more of the symptoms associated with the underlying disorder such that the patient reports an improvement in feeling or condition, notwithstanding that the patient may still be afflicted with the underlying disorder. Therapeutic benefit also generally includes halting or slowing the progression of the disease, regardless of whether improvement is realized.

The amount of compound(s) administered will depend upon a variety of factors, including, for example, the particular indication being treated, the mode of administration, whether the desired benefit is prophylactic or therapeutic, the severity of the indication being treated and the age and weight of the patient, the bioavailability of the particular compound(s) the conversation rate and efficiency into active drug compound under the selected route of administration, etc.

Determination of an effective dosage of compound(s) for a particular use and mode of administration is well within the capabilities of those skilled in the art. Effective dosages may be estimated initially from in vitro activity and metabolism assays. For example, an initial dosage of compound for use in animals may be formulated to achieve a circulating blood or serum concentration of the metabolite active compound that is at or above an IC₅₀ of the particular compound as measured in as in vitro assay. Calculating dosages to achieve such circulating blood or serum concentrations taking into account the bioavailability of the particular compound via the desired route of administration is well within the capabilities of skilled artisans. Initial dosages of compound can also be estimated from in vivo data, such as animal models. Animal models useful for testing the efficacy of the active metabolites to treat or prevent the various diseases described above are well-known in the art. Animal models suitable for testing the bioavailability and/or metabolism of compounds into active metabolites are also well-known. Ordinarily skilled artisans can routinely adapt such information to determine dosages of particular compounds suitable for human administration.

Dosage amounts will typically be in the range of from about 0.0001 mg/kg/day, 0.001 mg/kg/day or 0.01 mg/kg/day to about 100 mg/kg/day, but may be higher or lower, depending upon, among other factors, the activity of the active metabolite compound, the bioavailability of the compound, its metabolism kinetics and other pharmacokinetic properties, the mode of administration and various other factors, discussed above. Dosage amount and interval may be adjusted individually to provide plasma levels of the compound(s) and/or active metabolite compound(s) which are sufficient to maintain therapeutic or prophylactic effect. For example, the compounds may be administered once per week, several times per week (e.g., every other day), once per day or multiple times per day, depending upon, among other things, the mode of administration, the specific indication being treated and the judgment of the prescribing physician. In cases of local administration or selective uptake, such as local topical administration, the effective local concentration of compound(s) and/or active metabolite compound(s) may not be related to plasma concentration. Skilled artisans will be able to optimize effective local dosages without undue experimentation.

Definitions

The following terms and expressions used herein have the indicated meanings.

As used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.

Terms used herein may be preceded and/or followed by a single dash, or a double dash, “=”, to indicate the bond order of the bond between the named substituent and its parent moiety; a single dash indicates a single bond and a double dash indicates a double bond. In the absence of a single or double dash it is understood that a single bond is formed between the substituent and its parent moiety; further, substituents are intended to be read “left to right” unless a dash indicates otherwise. For example, C₁-C₆alkoxycarbonyloxy and —OC(O)C₁-C₆alkyl indicate the same functionality; similarly arylalkyl and -alkylaryl indicate the same functionality.

The term “alkenyl” as used herein, means a straight or branched chain hydrocarbon containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon-carbon double bond. Representative examples of alkenyl include, but are not limited to, ethenyl, 2-propenyl, 2-methyl-2-propenyl, 3-butenyl, 4-pentenyl, 5-hexenyl, 2-heptenyl, 2-methyl-1-heptenyl, 3-decenyl, and 3,7-dimethylocta-2,6-dienyl.

The term “alkoxy” as used herein, means an alkyl group, as defined herein, appended to the parent molecular moiety through an oxygen atom. Representative examples of alkoxy include, but are not limited to, methoxy, ethoxy, propoxy, 2-propoxy, butoxy, tert-butoxy, pentyloxy, and hexyloxy.

The term “alkyl” as used herein, means a straight or branched chain hydrocarbon containing from 1 to 10 carbon atoms unless otherwise specified. Representative examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec-butyl, iso-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl, n-hexyl, 3-methylhexyl, 2,2-dimethylpentyl, 2,3-dimethylpentyl, n-heptyl, n-octyl, n-nonyl, and n-decyl. When an “alkyl” group is a linking group between two other moieties, then it may also be a straight or branched chain; examples include, but are not limited to —CH₂—, —CH₂CH₂—, —CH₂CH₂CHC(CH₃)—, —CH₂CH(CH₂CH₃)CH₂—.

The term “alkynyl” as used herein, means a straight or branched chain hydrocarbon group containing from 2 to 10 carbon atoms and containing at least one carbon-carbon triple bond. Representative examples of alkynyl include, but are not limited, to acetylenyl, 1-propynyl, 2-propynyl, 3-butynyl, 2-pentynyl, and 1-butynyl.

The term “aryl,” as used herein, means a phenyl (i.e., monocyclic aryl), or a bicyclic ring system containing at least one phenyl ring or an aromatic bicyclic ring containing only carbon atoms in the aromatic bicyclic ring system. The bicyclic aryl can be azulenyl, naphthyl, or a phenyl fused to a monocyclic cycloalkyl, a monocyclic cycloalkenyl, or a monocyclic heterocyclyl. The bicyclic aryl is attached to the parent molecular moiety through any carbon atom contained within the phenyl portion of the bicyclic system, or any carbon atom with the napthyl or azulenyl ring. The fused monocyclic cycloalkyl or monocyclic heterocyclyl portions of the bicyclic aryl are optionally substituted with one or two oxo and/or thia groups. Representative examples of the bicyclic aryls include, but are not limited to, azulenyl, naphthyl, dihydroinden-1-yl, dihydroinden-2-yl, dihydroinden-3-yl, dihydroinden-4-yl, 2,3-dihydroindol-4-yl, 2,3-dihydroindol-5-yl, 2,3-dihydroindol-6-yl, 2,3-dihydroindol-7-yl, inden-1-yl, inden-2-yl, inden-3-yl, inden-4-yl, dihydronaphthalen-2-yl, dihydronaphthalen-3-yl, dihydronaphthalen-4-yl, dihydronaphthalen-1-yl, 5,6,7,8-tetrahydronaphthalen-1-yl, 5,6,7,8-tetrahydronaphthalen-2-yl, 2,3-dihydrobenzofuran-4-yl, 2,3-dihydrobenzofuran-5-yl, 2,3-dihydrobenzofuran-6-yl, 2,3-dihydrobenzofuran-7-yl, benzo[d][1,3]dioxol-4-yl, benzo[d][1,3]dioxol-5-yl, 2H-chromen-2-on-5-yl, 2H-chromen-2-on-6-yl, 2H-chromen-2-on-7-yl, 2H-chromen-2-on-8-yl, isoindoline-1,3-dion-4-yl, isoindoline-1,3-dion-5-yl, inden-1-on-4-yl, inden-1-on-5-yl, inden-1-on-6-yl, inden-1-on-7-yl, 2,3-dihydrobenzo[b][1,4]dioxan-5-yl, 2,3-dihydrobenzo[b][1,4]dioxan-6-yl, 2H-benzo[b][1,4]oxazin3(4H)-on-5-yl, 2H-benzo[b][1,4]oxazin3(4H)-on-6-yl, 2H-benzo[b][1,4]oxazin3(4H)-on-7-yl, 2H-benzo[b][1,4]oxazin3(4H)-on-8-yl, benzo[d]oxazin-2(3H)-on-5-yl, benzo[d]oxazin-2(3H)-on-6-yl, benzo[d]oxazin-2(3H)-on-7-yl, benzo[d]oxazin-2(3H)-on-8-yl, quinazolin-4(3H)-on-5-yl, quinazolin-4(3H)-on-6-yl, quinazolin-4(3H)-on-7-yl, quinazolin-4(3H)-on-8-yl, quinoxalin-2(1H)-on-5-yl, quinoxalin-2(1H)-on-6-yl, quinoxalin-2(1H)-on-7-yl, quinoxalin-2(1H)-on-8-yl, benzo[d]thiazol-2(3H)-on-4-yl, benzo[d]thiazol-2(3H)-on-5-yl, benzo[d]thiazol-2(3H)-on-6-yl, and, benzo[d]thiazol-2(3H)-on-7-yl. In certain embodiments, the bicyclic aryl is (i) naphthyl or (ii) a phenyl ring fused to either a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.

The terms “cyano” and “nitrile” as used herein, mean a —CN group.

The term “cycloalkyl” as used herein, means a monocyclic or a bicyclic cycloalkyl ring system. Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups can be saturated or unsaturated, but not aromatic. In certain embodiments, cycloalkyl groups are fully saturated. Examples of monocyclic cycloalkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, and cyclooctyl. Bicyclic cycloalkyl ring systems are bridged monocyclic rings or fused bicyclic rings. Bridged monocyclic rings contain a monocyclic cycloalkyl ring where two non-adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form —(CH₂)_(w)—, where w is 1, 2, or 3). Representative examples of bicyclic ring systems include, but are not limited to, bicyclo[3.1.1]heptane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and bicyclo[4.2.1]nonane. Fused bicyclic cycloalkyl ring systems contain a monocyclic cycloalkyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. The bridged or fused bicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkyl ring. Cycloalkyl groups are optionally substituted with one or two groups which are independently oxo or thia. In certain embodiments, the fused bicyclic cycloalkyl is a 5 or 6 membered monocyclic cycloalkyl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused bicyclic cycloalkyl is optionally substituted by one or two groups which are independently oxo or thia.

The term “halo” or “halogen” as used herein, means —Cl, —Br, —I or —F.

The term “haloalkyl” as used herein, means at least one halogen, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of haloalkyl include, but are not limited to, chloromethyl, 2-fluoroethyl, trifluoromethyl, pentafluoroethyl, and 2-chloro-3-fluoropentyl.

The term “heteroaryl,” as used herein, means a monocyclic heteroaryl or a bicyclic ring system containing at least one heteroaromatic ring. The monocyclic heteroaryl can be a 5 or 6 membered ring. The 5 membered ring consists of two double bonds and one, two, three or four nitrogen atoms and optionally one oxygen or sulfur atom. The 6 membered ring consists of three double bonds and one, two, three or four nitrogen atoms. The 5 or 6 membered heteroaryl is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heteroaryl. Representative examples of monocyclic heteroaryl include, but are not limited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, pyrazolyl, pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, and triazinyl. The bicyclic heteroaryl consists of a monocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. The fused cycloalkyl or heterocyclyl portion of the bicyclic heteroaryl group is optionally substituted with one or two groups which are independently oxo or thia. When the bicyclic heteroaryl contains a fused cycloalkyl, cycloalkenyl, or heterocyclyl ring, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon or nitrogen atom contained within the monocyclic heteroaryl portion of the bicyclic ring system. When the bicyclic heteroaryl is a monocyclic heteroaryl fused to a phenyl ring, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom within the bicyclic ring system. Representative examples of bicyclic heteroaryl include, but are not limited to, benzimidazolyl, benzofuranyl, benzothienyl, benzoxadiazolyl, benzoxathiadiazolyl, benzothiazolyl, cinnolinyl, 5,6-dihydroquinolin-2-yl, 5,6-dihydroisoquinolin-1-yl, furopyridinyl, indazolyl, indolyl, isoquinolinyl, naphthyridinyl, quinolinyl, purinyl, 5,6,7,8-tetrahydroquinolin-2-yl, 5,6,7,8-tetrahydroquinolin-3-yl, 5,6,7,8-tetrahydroquinolin-4-yl, 5,6,7,8-tetrahydroisoquinolin-1-yl, thienopyridinyl, 4,5,6,7-tetrahydrobenzo[c][1,2,5]oxadiazolyl, and 6,7-dihydrobenzo[c][1,2,5]oxadiazol-4(5H)-onyl. In certain embodiments, the fused bicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.

The term “heterocyclyl” or “heterocycle” as used herein, means a monocyclic heterocycle or a bicyclic heterocycle. The monocyclic heterocycle is a 3, 4, 5, 6 or 7 membered ring containing at least one heteroatom independently selected from the group consisting of O, N, and S where the ring is saturated or unsaturated, but not aromatic. The 3 or 4 membered ring contains 1 heteroatom selected from the group consisting of O, N and S.

The 5 membered ring can contain zero or one double bond and one, two or three heteroatoms selected from the group consisting of O, N and S. The 6 or 7 membered ring contains zero, one or two double bonds and one, two or three heteroatoms selected from the group consisting of O, N and S. The monocyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the monocyclic heterocycle. Representative examples of monocyclic heterocycle include, but are not limited to, azetidinyl, azepanyl, aziridinyl, diazepanyl, 1,3-dioxanyl, 1,3-dioxolanyl, 1,3-dithiolanyl, 1,3-dithianyl, imidazolinyl, imidazolidinyl, isothiazolinyl, isothiazolidinyl, isoxazolinyl, isoxazolidinyl, morpholinyl, oxadiazolinyl, oxadiazolidinyl, oxazolinyl, oxazolidinyl, piperazinyl, piperidinyl, pyranyl, pyrazolinyl, pyrazolidinyl, pyrrolinyl, pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl, thiadiazolinyl, thiadiazolidinyl, thiazolinyl, thiazolidinyl, thiomorpholinyl,1,1-dioxidothiomorpholinyl (thiomorpholine sulfone), thiopyranyl, and trithianyl. The bicyclic heterocycle is a monocyclic heterocycle fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocycle, or a monocyclic heteroaryl. The bicyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the monocyclic heterocycle portion of the bicyclic ring system. Representative examples of bicyclic heterocyclyls include, but are not limited to, 2,3-dihydrobenzofuran-2-yl, 2,3-dihydrobenzofuran-3-yl, indolin-1-yl, indolin-2-yl, indolin-3-yl, 2,3-dihydrobenzothien-2-yl, decahydroquinolinyl, decahydroisoquinolinyl, octahydro-1H-indolyl, and octahydrobenzofuranyl. Heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. In certain embodiments, the bicyclic heterocyclyl is a 5 or 6 membered monocyclic heterocyclyl ring fused to phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the bicyclic heterocyclyl is optionally substituted by one or two groups which are independently oxo or thia.

The term “nitro” as used herein, means a —NO₂ group.

The term “oxo” as used herein means a ═O group.

The term “saturated” as used herein means the referenced chemical structure does not contain any multiple carbon-carbon bonds. For example, a saturated cycloalkyl group as defined herein includes cyclohexyl, cyclopropyl, and the like.

The term “thia” as used herein means a ═S group.

The term “unsaturated” as used herein means the referenced chemical structure contains at least one multiple carbon-carbon bond, but is not aromatic. For example, a unsaturated cycloalkyl group as defined herein includes cyclohexenyl, cyclopentenyl, cyclohexadienyl, and the like.

Some compounds of the disclosure may tautomerize. Thus, the disclosure also comprises all tautomeric forms of the compounds disclosed herein. Some compounds of the disclosure may have chiral centers and/or geometric isomeric centers (E- and Z-isomers), and it is to be understood that the disclosure encompasses all such optical, enantiomeric, diastereoisomeric and geometric isomers.

“Pharmaceutically acceptable” refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problems or complications commensurate with a reasonable benefit/risk ratio or which have otherwise been approved by the United States Food and Drug Administration as being acceptable for use in humans or domestic animals.

“Pharmaceutically acceptable salt” refers to both acid and base addition salts.

“Therapeutically effective amount” refers to that amount of a compound which, when administered to a subject, is sufficient to effect treatment for a disease or disorder described herein. The amount of a compound which constitutes a “therapeutically effective amount” will vary depending on the compound, the disorder and its severity, and the age of the subject to be treated, but can be determined routinely by one of ordinary skill in the art.

“Treating” or “treatment” as used herein covers the treatment of a disease or disorder described herein, in a subject, preferably a human, and includes:

i. inhibiting a disease or disorder, i.e., arresting its development;

ii. relieving a disease or disorder, i.e., causing regression of the disorder;

iii. slowing progression of the disorder; and/or

iv. inhibiting, relieving, or slowing progression of one or more symptoms of the disease or disorder

“Subject” refers to a warm blooded animal such as a mammal, preferably a human, or a human child, which is afflicted with, or has the potential to be afflicted with one or more diseases and disorders described herein.

“Respiratory chain lesions” in mitochondria or “Mitochondria with respiratory chain lesions” refers to mitochondria in which the structures of the five complexes responsible for ATP production by oxidative phosphorylation are altered structurally, typically in a way that leads to diminished function.

Throughout this specification, unless the context requires otherwise, the word “comprise” and “include” and variations (e.g., “comprises,” “comprising,” “includes,” “including”) will be understood to imply the inclusion of a stated component, feature, element, or step or group of components, features, elements or steps but not the exclusion of any other integer or step or group of integers or steps.

Methods of Synthesis

Many general references providing commonly known chemical synthetic schemes and conditions useful for synthesizing the disclosed compounds are available (see, e.g., Smith and March, March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, Fifth Edition, Wiley-Interscience, 2001; or Vogel, A Textbook of Practical Organic Chemistry, Including Qualitative Organic Analysis, Fourth Edition, New York: Longman, 1978).

Compounds as described herein can be purified by any of the means known in the art, including chromatographic means, such as HPLC, preparative thin layer chromatography, flash column chromatography and ion exchange chromatography. Any suitable stationary phase can be used, including normal and reversed phases as well as ionic resins. Most typically the disclosed compounds are purified via silica gel and/or alumina chromatography. See, e.g., Introduction to Modern Liquid Chromatography, 2nd Edition, ed. L. R. Snyder and J. J. Kirkland, John Wiley and Sons, 1979; and Thin Layer Chromatography, ed E. Stahl, Springer-Verlag, New York, 1969.

During any of the processes for preparation of the subject compounds, it may be necessary and/or desirable to protect sensitive or reactive groups on any of the molecules concerned. This may be achieved by means of conventional protecting groups as described in standard works, such as J. F. W. McOmie, “Protective Groups in Organic Chemistry”, Plenum Press, London and New York 1973, in T. W. Greene and P. G. M. Wuts, “Protective Groups in Organic Synthesis”, Third edition, Wiley, New York 1999, in “The Peptides”; Volume 3 (editors: E. Gross and J. Meienhofer), Academic Press, London and New York 1981, in “Methoden der organischen Chemie”, Houben-Weyl, 4.sup.th edition, Vol. 15/1, Georg Thieme Verlag, Stuttgart 1974, in H.-D. Jakubke and H. Jescheit, “Aminosauren, Peptide, Proteine”, Verlag Chemie, Weinheim, Deerfield Beach, and Basel 1982, and/or in Jochen Lehmann, “Chemie der Kohlenhydrate: Monosaccharide and Derivate”, Georg Thieme Verlag, Stuttgart 1974. The protecting groups may be removed at a convenient subsequent stage using methods known from the art.

Representative synthetic procedures for the preparation of compounds of the disclosure are outlined below.

EXAMPLES

The compounds and methods of the disclosure are illustrated further by the following examples, which are provided for illustrative purposes and are not intended to be construed as limiting the disclosure in scope or spirit to the specific compounds and methods described in them.

Example 1

2-cyanophenothiazine (0.74 g, 3.30 mmol) was dissolved in 10 mL of anhydrous DMF. The mixture was cooled to 0° C. and 60% NaH (0.40 g, 9.90 mmol) was added. The dark mixture was stirred at 0° C. for an additional 15 min and Di-tert-butyl dicarbonate (0.90 g, 3.96 mmol) was added. The mixture was stirred at room temperature for 3 h and was diluted with 50 mL of brine. The aqueous layer was extracted with three 25 mL portions of ethyl acetate. The combined organic extract was dried over anhydrous MgSO₄ and concentrated under diminished pressure. The crude was purified on a silica gel column (10 cm×2 cm). Elution with ethyl acetate-hexane (1:9) gave 1 as a pale yellow solid: yield 1.07 g (100%); silica gel TLC R_(f)0.26 (ethyl acetate-hexane 1:9); ¹H NMR (CDCl₃) δ1.49 (s, 9H), 7.16-7.20 (m, 1H), 7.28-7.33 (m, 2H), 7.40 (s, 2H), 7.49 (d, 1H, J=8.4 Hz) and 7.80 (s, 1H); ¹³CNMR δ28.1, 83.1, 110.2, 118.2, 126.6, 127.2, 127.3, 127.5, 128.1, 129.1, 130.3, 130.6, 137.7, 139.0, 139.1 and 151.8; mass spectrum (APCI), m/z 325.1017 (M+H)⁺ (C₁₈H₁₇N₂O₂S requires m/z 325.1011).

Example 2

To a solution of the crude product in 10 mL of anhydrous CH₂Cl₂ was added 4.0 mL (4.0 mmol) of 1M DIBAL-H in toluene dropwise at −78° C. The mixture was stirred at −78° C. for 3 h and was diluted with 2N HCl. The aqueous layer was extracted with three 30 mL portions of CH₂Cl₂. The combined organic extract was dried over anhydrous MgSO₄ and was concentrated under diminished pressure. The residue was purified on a silica gel column (7 cm×4 cm). Elution with 1:9 ethyl acetate-hexanes afforded 2 as a yellow solid: yield 0.63 g (58%); silica gel TLC R_(f)0.17 (ethyl acetate-hexane 1:9); ¹H NMR (CDCl₃) δ1.48 (s, 9H), 7.14-7.18 (m, 1H), 7.26-7.32 (m, 2H), 7.44 (d, 1H, 7=8.0 Hz), 7.52 (d, 1H, 7=7.4 Hz), 7.64 (d, 1H, 7=8.0 Hz), 7.99 (s, 1H) and 9.96 (s, 1H); ¹³C NMR δ28.1, 82.8, 126.5, 126.6, 127.1, 127.3, 127.4, 127.8, 128.3, 130.5, 135.1, 137.9, 139.1, 140.2 and 152.1; mass spectrum (ESI), m/z 328.0823 (M+Na)⁺ (C₁₈H₁₇NO₃SNa requires m/z 328.0827).

Example 3

To a solution of hexadecyltriphenylphosphonium bromide (0.64 g, 1.13 mmol) in 5 mL of anhydrous THF at −78° C. was added 1.20 mL (1.20 mmol) of 1M sodium bis-(trimethylsilyl)amide in THF dropwise. The yellow mixture was stirred at 0° C. for 3 h and was cooled to −78° C. To this bright orange suspension was added 2 (0.37 g, 1.13 mmol) dissolved in 5 mL of anhydrous THF dropwise. The light yellow mixture was stirred at 0° C. under argon atmosphere overnight and was diluted with 50 mL of brine. The aqueous layer was extracted with three 25 mL portions of ethyl acetate. The combined organic extract was dried over anhydrous MgSO₄ and was concentrated under diminished pressure. The residue was purified on a silica gel column. Elution with 1:9 CH₂C₁₋₂-hexanes yielded a cis-trans mixture as a white solid.

To a solution of the cis-trans mixture (0.41 g, 0.77 mmol) in 3:7 CH₂C₁₋₂-ethanol was added palladium on carbon (26 mg, 0.16 mmol). The suspension was stirred at room temperature under H₂ atmosphere (40 psi) for 2 h. The mixture was filtered through celite pad. The filtrate was concentrated under diminished pressure to afford 3 as a white solid: yield 0.41 g (74% over two steps); silica gel TLC R_(f)0.1 (CH₂C₁₋₂-hexane 1:9); ¹H NMR (CDCl₃)<70.88 (t, 3H, J=7.0 Hz), 1.26-1.30 (m, 28H), 1.49 (s, 9H), 1.60 (t, 2H, J=7.2 Hz), 2.59 (t, 2H, J=7.6 Hz), 6.96 (d, 1H, J=7.6 Hz), 7.12 (t, 1H, J=7.6 Hz), 7.21-7.26 (m, 2H), 7.32-7.35 (m, 2H) and 7.52 (d, 1H, J=7.6 Hz); ¹³C NMR (CDCl₃)<714.3, 22.9, 28.4, 29.5, 29.53, 29.70, 29.74, 29.84, 29.87, 31.7, 32.1, 35.8, 82.0, 126.1, 126.5, 126.6, 127.2, 127.33, 127.37, 127.6, 128.9, 132.7, 138.8, 139.0, 142.0 and 152.7; mass spectrum (MALDI-TOF), in z 537.3575 (M+H)⁺ (C₃₄H₅₁NO₂S requires in z 537.3641).

Example 4

To a solution of 3 (0.23 g, 0.43 mmol) in 8 mL of anhydrous CH₂Cl₂ was added 0.26 mL (3.44 mmol) of trifluoroacetic acid dropwise. The mixture was stirred at room temperature for 12 h under argon atmosphere and was neutralized with 50 mL of saturated NaHCO₃ solution. The aqueous layer was extracted with three 30 mL portions of CH₂Cl₂. The combined organic layer was dried over anhydrous MgSO₄ and was concentrated under diminished pressure. The crude (4) was utilized in the next step without further purification.

Example 5

N-(7-(dimethylamino)-2-heptadecyl-3H-phenothiazin-3-ylidene)-N-methylmethan-aminium iodide (5)

To a solution 45 mg of the crude 4 in 5 mL of CH₂Cl₂ was added 81 mg (0.32 mmol) of iodine followed by 0.25 mL (0.5 mmol) of 2M Dimethylamine in THF. The mixture was stirred at room temperature under argon atmosphere for 12 h. The greenish blue mixture was purified on a silica gel column (10 cm×2 cm). Elution with ethyl acetate afforded 5 as a green solid: yield 18 mg (28%); silica gel TLC R_(f)0.4 (ethyl acetate); ¹H NMR (CDCl₃) δ0.86 (t, 3H, J=6.6 Hz), 1.15-1.37 (m, 28H), 1.69-1.72 (m, 2H), 2.81-2.85 (m, 2H), 3.33 (s, 6H), 3.46 (s, 6H), 7.36-7.38 (m, 1H), 7.41 (s, 1H), 7.76 (m, 1H), 7.89 (s, 1H), 7.99 (d, 1H, J=7.6 Hz); mass spectrum (MALDI-TOF), m/z 522.3978 (M)⁺ (C₃₃H₅₂N₃S requires m/z 522.3876).

Example 6

N-(4,7-bis(dimethylamino)-2-heptadecyl-3H-phenothiazin-3-ylidene)-N-methylmethanaminium iodide (6)

To a solution 0.10 g of the crude (4) in 5 mL of anhydrous CH₂Cl₂ was added 0.19 g (0.74 mmol) of iodine followed by 1.15 mL (2.3 mmol) of 2M Dimethylamine in THF. The mixture was heated at 45 under argon atmosphere for 7 h. The blue mixture was purified on a silica gel column (10 cm×2 cm). Elution with 20% methanol in ethyl acetate afforded 6 as a blue solid: yield 40 mg (31%); silica gel TLC R_(f)0.35 (ethyl acetate-methanol 4:1); ¹H NMR (CDCl₃) 50.86 (t, 3H, J=6.8 Hz), 1.24-1.44 (m, 28H), 1.61-1.63 (m, 2H), 2.71 (m, 2H), 3.28 (s, 6H), 3.30 (s, 6H), 3.49 (s, 6H), 6.17 (s, 1H), 6.89 (d, 1H, J=2.8 Hz), 7.05 (dd, J=9.2 Hz, J=2.4 Hz), 7.78 (d, 1H, J=9.6 Hz); ¹³C NMR S 14.3, 22.8, 26.4, 29.5, 29.8, 29.82, 29.85, 30.1, 30.7, 32.1, 41.4, 44.7, 45.9, 51.0, 101.3, 105.6, 115.8, 121.5, 130.6, 131.1, 132.2, 133.8, 137.0, 153.5 and 161.1; mass spectrum (MALDI-TOF), m/z 565.4135 (M)^(+(C) ₃₅H₅₇N₄S requires m/z 565.4298).

Example 7

7-(dimethylamino)-2-heptadecyl-3H-phenothiazin-3-one (7)

To a dark green solution of 5 (70 mg, 0.09 mmol) in 3.5 mL THF-H₂O (6:1) was added KOH (30 mg, 0.53 mmol). The mixture was stirred for 2 minute at room temperature until it changes from green to red. The aqueous layer was extracted with EtOAc. The organic layer was dried over anhydrous MgSO₄ and was concentrated under diminished pressure. The crude was purified on a silica gel column (7 cm×2 cm). Elution with 2:3 EtOAc-hexane yielded 7 as a violet solid: yield-11 mg (24%); silica gel TLC A/0.59 (ethyl acetate-hexane 2:3); ¹H NMR (CDCl₃) δ 0.86-0.89 (m, 3H), 1.27-1.41 (m, 28H), 1.72 (t, 2H, J=6.0 Hz), 2.72 (t, 2H, J=6.4 Hz), 2.89 (s, 6H), 6.73 (d, 1H, J=1.6 Hz), 6.89 (dd, 1H, J=7.6 Hz, J=2.0 Hz), 6.93 (s, 1H), 7.60 (d, 1H, J=8.0 Hz) and 7.71 (s, 1H); ¹³C NMR (CDCl₃) δ 14.3, 22.8, 29.5, 29.6, 29.7, 29.81, 29.85, 30.1, 31.6, 32.1, 44.0,112.8,119.3, 123.3, 134.0, 134.6, 135.5, 136.4, 139.7, 143.3, 155.8 and 182.5; mass spectrum (ESI), m/z 495.3414 (M+H)^(+(C) ₃₁H₄₇N₂OS requires m/z 495.3409).

Example 8

1-(2-heptadecyl-7-(piperidin-1-yl)-3H-phenothiazin-3-ylidene)piperidin-1-ium iodide (8)

Crude 4 (30 mg, 0.07 mmol) was dissolved in 5 mL CH₂Cl₂ and I₂ (56 mg, 0.22 mmol) was added followed by piperidine (34 μL, 0.35 mmol). The mixture was stirred at room temperature for 3 h under argon atmosphere and was purified on a silica gel column (8 cm×2 cm). Elution with ethyl acetate gave 8 as a green solid: yield-5 mg (10%); silica gel TLC R_(f) 0.43 (ethyl acetate); ¹H NMR (CDCl₃) δ 0.86-0.89 (m, 3H), 1.24-1.40 (m, 28H), 1.76-1.80 (m, 2H), 2.76 (t, 2H, J=7.8 Hz), 3.43-3.45 (m, 3H), 3.92-3.98 (m, 1H), 7.56 (s, 1H), 7.61-7.64 (m, 1H), 7.69 (d, 1H, J=2.0 Hz), 8.06 (s, 1H) and 8.13 (d, 1H, J=9.6 Hz); mass spectrum (MALDI-TOF), m/z 602.4560 (M)⁺ (C₃₉H₆₀N₃S requires m/z 602.4502).

Example 9

2-heptadecyl-7-(piperidine-1-yl)-3H-phenothiazin-3-one (9)

To a dark green solution of 8 (60 mg, 0.1 mmol) in 3.5 mL THF-H₂O (6:1) was added KOH (16 mg, 0.3 mmol). The mixture was stirred for 2 minute at room temperature until it changes from green to red. The aqueous layer was extracted with EtOAc. The organic layer was dried over anhydrous MgSO₄ and was concentrated under diminished pressure. The crude was purified on a silica gel column (7 cm×2 cm). Elution with 1:4 ethyl acetate-hexane yielded 9 as a brownish solid: yield-12.3 mg (22%); silica gel TLC A/0.75 (ethyl acetate-hexane 3:2); ¹H NMR (CDCl₃) δ 0.86-0.88 (m, 3H), 1.22-1.38 (m, 28H), 1.62-1.67 (m, 8H), 2.64 (t, 2H, J=8.0 Hz), 2.96 (t, 2H, J=4.8 Hz), 6.71 (d, 1H, J=2.0 Hz), 6.87 (dd, 1H, J=12 Hz, J=2.0 Hz), 6.94 (s, 1H), 7.57 (d,1H, J=10 Hz) and 7.70 (s, 1H); ¹³C NMR (CDCl₃) S 14.1, 22.6, 22.7, 24.1, 26.1, 29.3, 29.4, 29.5, 29.54, 29.6, 29.63, 29.67, 30.2, 30.5, 31.6, 31.9, 53.5, 114.1 119.1, 122.9, 134.0, 134.9, 135.0, 137.0, 139.6, 143.6, 156.1 and 182.3; mass spectrum (ESI), m/z 535.3731 (M+H)⁺ (C₃₄H₅₁N₂OS requires m/z 535.3722).

Example 10

4-(2-heptadecyl-7-morpholino-3H-phenothiazin-3-ylidene)morpholin-4-ium iodide (10)

Crude 4 (44 mg, 0.10 mmol) was dissolved in 5 mL CH₂Cl₂ and I₂ (81 mg, 0.32 mmol) was added followed by morpholine (47 μL, 0.50 mmol). The mixture was stirred at room temperature for 3 h under argon atmosphere and was purified on a silica gel column. Elution with ethyl acetate gave 10 as a green solid: yield-5 mg (7%); silica gel TLC R_(f)0.43 (ethyl acetate); ¹H NMR (CDCl₃) δ 0.86 (m, 3H), 1.24-1.40 (m, 28H), 1.76-1.80 (m, 2H), 2.76 (t, 2H, J=7.8 Hz), 3.43-3.45 (m, 3H), 3.92-3.98 (m, 1H), 7.56 (s, 1H), 7.61-7.64 (m, 1H), 7.69 (d, 1H, J=2.0 Hz), 8.06 (s, 1H) and 8.13 (d, 1H, 7=9.6 Hz); ¹³C NMR (CDCl₃) δ 14.1, 22.7, 29.3, 29.4, 29.5, 29.6, 29.7, 30.1, 30.9, 31.9, 32.1, 48.9, 52.3, 66.6, 107.7, 113.7, 121.2, 130.9, 137.6, 137.9, 139.7, 139.8, 140.1, 153.9 and 157.9; mass spectrum (ESI), m/z 606.4113 (M)⁺ (C₃₇H₅₆N₃O₂S requires m/z 606.4093).

Example 11

2-heptadecyl-7-(morpholine-1-yl)-3H-phenothiazin-3-one (11)

To a dark green solution of 10 (58 mg, 0.1 mmol) in 3.5 mL THF-H₂O (6:1) was added KOH (11 mg, 0.19 mmol). The mixture was stirred for 2 minute at room temperature until it changes from green to red. The aqueous layer was extracted with EtOAc. The organic layer was dried over anhydrous MgSO₄ and was concentrated under diminished pressure. The crude was purified on a silica gel column. Elution with 1:4 ethyl acetate-hexane yielded 11 as a brownish solid: yield-7 mg (14%); silica gel TLC A/0.75 (ethyl acetate-hexane 3:2); ¹H NMR (CDCl₃) δ 0.86 (m, 3H), 1.21-1.38 (m, 28H), 1.69-1.70 (m, 2H), 2.67 (t, 2H, J=8.0 Hz), 2.99-3.02 (m, 4H), 3.86-3.88 (m, 4H), 6.72 (d, 1H, J=2.0 Hz), 6.89 (dd, 1H, J=10.2 Hz, J=2.2 Hz), 6.97 (s, 1H), 7.58 (d,1H, 7=10 Hz) and 7.74 (s, 1H); mass spectrum (ESI), m/z 537.3518 (M+H)⁺ (C₃₃H₄₉N₂O₂S requires m/z 537.3515).

Example 12

N-(4,7-bis(morpholino)-2-heptadecyl-3H-phenothiazin-3-ylidene)-N-morpholinium iodide (12)

4 (0.20 g, 0.45 mmol) was dissolved in dichloromethane. Iodine (0.37 g, 1.46 mmol) was added and the reaction was run in the dark for 15 minutes. Thereafter, morpholine (0.20 ml (0.20 g), 2.28 mmol) was added dropwise and the reaction was allowed to run for 4 h. The product was dissolved in dichloromethane and the solution was concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×3 cm). Elution with at 1:1 ethylacetate/methanol afforded N-(4,7-bis(morpholino)-2-heptadecyl-3H-phenothiazin-3-ylidene)-N-morpholinium iodide (12) as a blue violet solid: yield 0.10 g (27%); silica gel TLC R_(f) 0.48 (1:1 ethylacetate/methanol); ¹H NMR (CDCl₃) (500 MHz) S 0.85 (t, 3H, J=6.7 Hz), 1.23 (s, 30H), 1.70 (m, 2H), 2.68 (t, 2H, J=8 Hz), 3.18 (t, 3H, J=4.5 Hz), 3.27 (t, 2H, J=5 Hz), 3.78 (t, 3H, J=4.5 Hz), 3.88 (t, 3H, J=4.5 Hz), 3.93 (t, 3H, J=4.7 Hz), 3.98 (t, 3H, J=4.5 Hz), 4.04 (s, 3H), 4.12 (t, 2H, J=5 Hz), 6.51 (d, 1H, J=2.5 Hz), 7.29 (s, 1H) and 7.69 (s, 2H); ¹³C NMR (CDCl₃) (125 MHz) S 14.24, 22.80, 29.46, 29.56, 29.81, 30.44, 31.38, 32.03, 42.98, 49.57, 52.39, 52.81, 62.98, 66.82, 66.92, 101.97, 107.21, 114.29, 127.58, 134.53, 136.29, 136.69, 137.32, 138.84, 155.56, 156.95 and 157.04; mass spectrum (APCI), m/z (M+2H)⁺693.4799 (C₄₁H₆₅N₄O₃S requires 693.4777); ultraviolet/visible spectrum λ_(max) 589.9 nm (in dichloromethane), λ_(max) 575.0 nm (in methanol).

Example 13

4,7-bis(morpholino)-2-heptadecyl-3H-phenothiazin-3-one (13)

12 (0.10 g, 0.14 mmol) was dissolved in a mixture of tetrahydrofuran/water (6:1). Solid KOH (0.008 g, 0.14 mmol) was added and the reaction mixture was stirred for 10 minutes. As soon as the reaction mixture changed colour from blue-violet to chocolate brown, the reaction was quenched with water. The product was extracted in ethyl acetate, washed with brine, dried (Na₂SO₄) and was concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×1 cm). Elution with at 4:1 hexane/ethylacetate afforded 4,7-bis(morpholino)-2-heptadecyl-3H-phenothiazin-3-one (13) as a chocolate brown solid: yield 0.01 g (20%); silica gel TLC R_(f) 0.37 (ethylacetate); ¹H NMR (CDCl₃) (500 MHz) S 0.87 (t, 3H, J=6.7 Hz), 1.25 (s, 30H), 1.68 (m, 2H), 2.66 (t, 2H, J=8 Hz), 2.99 (t, 2H, J=4.5 Hz), 3.37 (t, 3H, J=4 Hz), 3.87 (t, 3H, J=4 Hz), 3.95 (t, 3H, J=4.25 Hz), 6.11 (s, 1H), 6.53 (s, 1H), 6.93 (s, 1H) and 7.57 (s, 1H); ¹³C NMR (CDCl₃) (125 MHz) S 14.27, 22.84, 29.51, 29.62, 29.85, 30.59, 32.07, 51.83, 52.72, 66.78, 67.14, 114.65, 115.43, 119.83, 122.98, 133.93, 134.19, 135.11, 137.55, 141.10, 154.37, 156.01 and 182.38; mass spectrum (APCI), m/z (M+H)⁺622.4033 (C₃₇H₅₆N₃O₃S requires 622.4042); ultraviolet/visible spectrum λ_(max) 474.9 nm (in dichloromethane), λ_(max) 475.0 nm (in methanol).

Example 14

N-(7-(azetidino)-2-heptadecyl-3H-phenothiazin-3-ylidene)-N-azetidinium iodide (14)

The azetidine hydrochloride (0.21 g, 2.33 mmol) was dissolved in methanol. Sodium carbonate was added to it until the solution was basic (tested by pH paper). The residual excess sodium carbonate was separated from the azetidine solution by decantation. This azetidine in methanol solution was directly used for the reaction. 4 (0.20 g, 0.46 mmol) was dissolved in dichloromethane. Iodine (0.37 g, 1.49 mmol) was added and the reaction was run in the dark for 15 minutes. Thereafter, azetidine (dissolved in methanol) was added dropwise and the reaction was allowed to run for 4 h. The product was dissolved in dichloromethane and the solution was concentrated under diminished pressure. The crude product N-(7-(azetidino)-2-heptadecyl-3H-phenothiazin-3-ylidene)-N-azetidinium iodide (14) was obtained as a dirty green solid. Mass spectrum (MALDI-TOF), m/z (M⁺) 546.957 (C₃₅H₅₂N₃S requires 546.3876).

Example 15

7-(azetidino)-2-heptadecyl-3H-phenothiazin-3-one (15)

14 (0.06 g, 0.10 mmol) was dissolved in a mixture of tetrahydrofuran/water (6:1). Solid KOH (0.006 g, 0.10 mmol) was added and the reaction mixture was stirred for 10 minutes. As soon as the reaction mixture changed colour from green to red, the reaction was quenched with water. The product was extracted in ethyl acetate, washed with brine, dried (Na₂SO₄) and was concentrated under diminished pressure. The crude product 7-(azetidino)-2-heptadecyl-3H-phenothiazin-3-one (15) was obtained as a light red solid. Mass spectrum (MALDI-TOF), m/z (M+H)⁺507.952 (C₃₂H₄₇N₂OS requires 507.3331).

Example 16

[0143] (1-butyl)triphenylphosphonium bromide (2.30 g, 5.81 mmol) was dissolved in anhydrous tetrahydrofuran. The reaction medium was cooled to −78° C. and sodium bis(trimethylsilyl) amide (5.81 ml (5.22 g), 5.81 mmol) was added dropwise. The reaction mixture was stirred at 0° C. for 3 h. Thereafter, the mixture was cooled to −78° C. and 2 (1.90 g, 5.81 mmol), pre-dissolved in anhydrous tetrahydrofuran was added. The reaction mixture was stirred at 0° C. for 18 h. The product was extracted with dichloromethane. The organic phase was washed with brine, dried (Na₂SO₄) and concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×3 cm). Elution with 4:1 hexane/dichloromethane afforded the pure product as a yellow solid: yield 1.30 g (62%); silica gel TLC R_(f) 0.66 (9:1 hexane/dichloromethane); ¹H NMR (CDCl₃) (500 MHz) S 1.03 (t, 3H, J=12 Hz), 1.57 (s, 11H), 2.42 (q, 2H, J=7 Hz), 5.75 (m, 1H), 6.48 (d, 1H,J=2 Hz), 7.15 (m, 2H), 7.32 (m, 3H), 7.58 (s, 1H) and 7.63 (d, 1H, J=8 Hz); ¹³C NMR (CDCl₃) (125 MHz) S 13.60, 22.83, 27.88, 30.38, 81.53, 125.75, 126.19, 126.33, 126.70, 127.07, 127.23, 127.74, 127.81, 129.72, 131.88, 133.23, 136.29, 138.27, 138.51 and 152.07; mass spectrum (APCI), m/z (M+H)⁺368.1680 (C₂₂H₂₆NO₂S requires 368.1684).

The product from the previous step (1.90 g, 5.31 mmol) was dissolved in 7:3 ethanol/dichloromethane and purged under argon gas for 20 minutes. Palladium on carbon (0.11 g, 1.06 mmol) was added. The reaction was done for 2 h under 40 psi pressure in a parahydrogenator. On completion of the reaction, the product was separated from the catalyst by filtration through a celite pad using methanol as the solvent. The product solution was then concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×3 cm). Elution with 4:1 hexane/dichloromethane afforded tert-butyl-2-pentyl-10H-phenothiazine-10-carboxylate (16) as a colourless oil: yield 1.70 g (87%); silica gel TLC R_(f) 0.62 (9:1 hexane/dichloromethane); ¹H NMR (CD₃OD) (500 MHz) S 0.76 (s, 3H), 1.16 (s, 4H), 1.32 (s, 9H), 1.45 (s, 2H), 2.41 (s, 2H), 6.77 (s, 1H), 6.94 (s, 1H), 7.05 (m, 2H), 7.14 (s, 1H), 7.23 (s, 1H) and 7.38 (s, 1H); ¹³C NMR (CD₃OD) (125 MHz) S 14.61, 23.49, 28.58, 32.14, 32.39, 36.37, 82.85, 127.09, 127.46, 128.00, 128.26, 128.31, 129.94, 133.51, 139.70, 139.90, 142.78 and 153.64; mass spectrum (APCI), m/z (M+H)⁺370.1842 (C₂₂H₂₈NO₂S requires 370.1841).

Example 17

16 (1.70 g, 4.60 mmol) was dissolved in anhydrous dichloromethane. Trifluoroacetic acid (2.81 ml (4.18 g), 36.80 mmol) was added dropwise. The reaction mixture was stirred at room temperature for 18 h. The product was mixed with sodium bicarbonate, extracted with dichloromethane, dried (Na₂SO₄) and then concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×3 cm). Elution with 9:1 hexane/ethyl acetate afforded 2-pentyl-10H-phenothiazine (17) as a white solid: yield 13 mg (1%); silica gel TLC R_(f) 0.88 (1:1 hexane/ethylacetate); mass spectrum (APCI), m/z (M+H)^(+270.1315 (C) ₁₇H₂₀NS requires 270.1316).

Example 18

N-(7-(dimethylamino)-2-pentyl-3H-phenothiazin-3-ylidene)-N-methyl methanaminium iodide (18)

17 (0.18 g, 0.66 mmol) was dissolved in dichloromethane. Iodine (0.54 g, 2.14 mmol) was added and the reaction was run in the dark for 15 minutes. Thereafter, dimethylamine (1.7 ml (1.13 g), 3.34 mmol) was added dropwise and the reaction was allowed to run for 4 h. The product was dissolved in dichloromethane and the solution was concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×3 cm). Elution with at 1:1 methanol/acetonitrile afforded N-(7-(dimethylamino)-2-pentyl-3H-phenothiazin-3-ylidene)-N-methyl methanaminium iodide (18) as a green solid: yield 0.04 g (25%); silica gel TLC R_(f) 0.23 (acetonitrile); ¹H NMR (CDCl₃) (500 MHz) S 0.85 (t, 3H, J=6.5 Hz), 1.33 (s, 4H), 1.64 (s, 2H), 2.60 (s, 3H), 2.80 (s, 2H), 3.41 (d, 9H, J=64.5 Hz), 7.29 (s, 2H), 7.79 (d, 2H, J=49.5 Hz) and 8.67 (s, 1H); ¹³C NMR (CDCl₃) (125 MHz) S 13.95, 22.38, 29.74, 31.53, 33.89, 34.82, 44.64, 106.93, 111.08, 119.92, 131.55, 135.27, 136.79, 137.03, 137.19, 138.40, 138.75, 153.80 and 157.80; mass spectrum (APCI), m/z (M+2H)⁺356.2170 (C₂₁H₃₀N₃S requires 356.2160); ultraviolet/visible spectrum λ_(max) 665.0 nm (in dichloromethane), λ_(max) 665.0 nm (in methanol).

Example 19

7-(dimethylamino)-2-pentyl-3H-phenothiazin-3-one (19)

18 (0.65 g, 1.85 mmol) was dissolved in a mixture of tetrahydrofuran/water (6:1). Solid KOH (0.10 g, 1.85 mmol) was added and the reaction mixture was heated and stirred until the reaction mixture changed colour from green to red. The reaction was quenched with water. The product was extracted in ethyl acetate, washed with brine, dried (Na₂SO₄) and was concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×1 cm). Elution with ethylacetate afforded 7-(dimethylamino)-2-pentyl-3H-phenothiazin-3-one (19) as a red solid: yield 0.02 g (5%); silica gel TLC R_(f) 0.16 (4:1 hexane/ethyl acetate); ¹H NMR (CDCl₃) (400 MHz) S 0.91 (t, 3H, J=7 Hz), 1.37 (m, 4H), 1.71 (m, 2H), 2.70 (t, 2H, J=8 Hz), 2.87 (s, 4H), 6.71 (d, 1H, J=2 Hz), 6.88 (dd, 1H, J=2.2 Hz), 6.91 (s, 1H), 7.58 (d, 1H, J=10 Hz) and 7.70 (s, 1H); ¹³C NMR (CDCl₃) (100 MHz) S 14.18, 22.69, 29.79, 31.59, 31.99, 44.02, 112.83, 119.27, 123.32, 133.98, 134.56, 135.45, 136.39, 139.71, 143.29, 155.83 and 182.44; mass spectrum (APCI), m/z (M+H)^(+327.1534 (C) ₁₉H₂₃N₂OS requires 327.1531); ultraviolet/visible spectrum λ_(max) 545.0 nm (in dichloromethane), λ_(max) 570.0 nm (in methanol).

Example 20

(1-decyl)triphenylphosphonium bromide (0.79 g, 1.64 mmol) was dissolved in anhydrous tetrahydrofuran. The reaction medium was cooled to −78° C. and sodium bis(trimethylsilyl) amide (1.64 ml (1.47 g), 1.64 mmol) was added dropwise. The reaction mixture was stirred at 0° C. for 3 h. Thereafter, the mixture was cooled to −78° C. and 2 (0.53 g, 1.64 mmol), pre-dissolved in anhydrous tetrahydrofuran was added. The reaction mixture was stirred at 0° C. for 18 h. The product was extracted with dichloromethane. The organic phase was washed with brine, dried (Na₂SO₄) and concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×1 cm). Elution with 4:1 hexane/dichloromethane afforded the pure product as a yellow solid: yield 0.14 g (20%); ¹H NMR (CDCl₃) (400 MHz) S 0.93 (t, 3H, J=6.4 Hz), 1.31 (s, 13H), 1.53 (s, 10H), 2.38 (q, 2H, J=1 Hz), 5.71 (m, 1H), 6.40 (d, 1H, J=11.2 Hz), 7.13 (m, 2H), 7.28 (q, 2H, J=7.4 Hz), 7.35 (d, 1H, J=7.6 Hz), 7.49 (s, 1H) and 7.57 (d, 1H, J=7.6 Hz); ¹³C NMR (CDCl₃) (100 MHz) S 14.26, 22.84, 27.36, 28.32, 29.48, 29.73, 29.78, 29.93, 30.07, 32.07, 82.10, 126.14, 126.64, 127.36, 127.54, 127.81, 127.90, 129.99, 130.02, 130.06, 132.34, 134.01, 136.79, 138.65, 138.92 and 152.59; mass spectrum (APCI), m/z (M+H)⁺452.2617 (C₂₈H₃₈NO₂S requires 452.2623).

The pure product from the previous step (0.85 g, 1.88 mmol) was dissolved in 7:3 ethanol/dichloromethane and purged under argon gas for 20 minutes. Palladium on carbon (0.04 g, 0.37 mmol) was added. The reaction was done for 2 h under 40 psi pressure in a parahydrogenator. On completion of the reaction, the product was separated from the catalyst by filtration through a celite pad using methanol as the solvent. The product solution was then concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×1 cm). Elution with 4:1 hexane/dichloromethane afforded tert-butyl-2-undecyl-10H-phenothiazine-10-carboxylate (20) as a colourless oil: yield 0.54 g (80%); ³H NMR (CDCl₃) (500 MHz) S 0.97 (t, 3H, J=6.7 Hz), 1.35 (s, 16H), 1.56 (s, 8H), 1.69 (m, 2H), 2.67 (t, 2H, J=7.7 Hz), 7.02 (d, 1H, J=8 Hz), 7.16 (t, 1H, J=7.7 Hz), 7.28 (d, 2H, J=8 Hz), 7.37 (d, 1H, J=8 Hz), 7.44 (s, 1H) and 7.60 (d, 1H, J=7.5 Hz); ¹³C NMR (CDCl₃) (125 MHz) S 14.12, 22.69, 28.17, 29.28, 29.34, 29.51, 29.57, 29.64, 29.67, 31.49, 31.92, 35.58, 81.70, 125.88, 126.27, 126.99, 127.06, 127.11, 127.19, 127.36, 128.79, 132.46, 138.65, 138.86, 141.67 and 152.41; mass spectrum (APCI), m/z (M+H)⁺454.2772 (C₂₈H₄₀NO₂S requires 454.2780).

Example 21

20 (0.82 g, 1.81 mmol) was dissolved in anhydrous dichloromethane. Trifluoroacetic acid (1.10 ml (1.63 g), 14.48 mmol) was added dropwise. The reaction mixture was stirred at room temperature for 18 h. The product was mixed with sodium bicarbonate, extracted with dichloromethane, dried (Na₂SO₄) and then concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×1 cm). Elution with 9:1 hexane/ethyl acetate afforded 2-undecyl-10H-phenothiazine (21) as a white solid: yield 0.13 g (100%); mass spectrum (APCI), m/z (M+H)⁺354.2252 (C₂₃H₃₂NS requires 354.2255).

Example 22

N-(7-(dimethylamino)-2-undecyl-3H-phenothiazin-3-ylidene)-N-methyl methanaminium iodide (22)

21 (1.40 g, 4.00 mmol) was dissolved in dichloromethane. Iodine (3.20 g, 12.90 mmol) was added and the reaction was run in the dark for 15 minutes. Thereafter, dimethylamine (10.10 ml (6.70 g), 20.30 mmol) was added dropwise and the reaction was allowed to run for 4 h. The product was dissolved in dichloromethane and the solution was concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×3 cm). Elution with methanol afforded N-(7-(dimethylamino)-2-undecyl-3H-phenothiazin-3-ylidene)-N-methyl methanaminium iodide (22) as a green solid: yield 0.10 g (25%); silica gel TLC R_(f) 0.07 (methanol); ¹H NMR (CDCl₃) (500 MHz) S 0.88 (t, 3H, J=6.7 Hz), 1.26 (s, 18H), 1.72 (m, 2H), 2.85 (t, 2H, J=7.7 Hz), 3.35 (s, 4H), 3.46 (s, 4H), 3.56 (s, 1H), 7.28 (d, 1H, J=12.5 Hz), 7.37 (s, 1H), 7.39 (s, 1H), 7.87 (s, 1H) and 7.97 (d, 1H, J=10 Hz); ¹³C NMR (CDCl₃) (125 MHz) S 14.25, 22.79, 29.45, 29.59, 29.68, 29.71, 29.73, 30.26, 32.01, 34.28, 42.57, 44.88, 106.88, 111.25, 119.95, 132.00, 135.74, 137.12, 137.30, 137.49, 138.71, 138.89, 154.21 and 158.23; mass spectrum (APCI), m/z (M+2H)^(+440.3087 (C) ₂₇H₄₂N₃S requires 440.3099); ultraviolet/visible spectrum λ_(max) 669.9 nm (in dichloromethane), λ_(max) 665.0 nm (in methanol).

Example 23

7-(dimethylamino)-2-undecyl-3H-phenothiazin-3-one (23)

22 (0.08 g, 0.18 mmol) was dissolved in a mixture of tetrahydrofuran/water (6:1). Solid KOH (0.01 g, 0.18 mmol) was added and the reaction mixture was stirred for 10 minutes when the colour changed from green to red. The reaction was quenched with water. The product was extracted in ethyl acetate, washed with brine, dried (Na₂SO₄) and was concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×1 cm). Elution with 4:1 hexane/ethylacetate afforded 7-(dimethylamino)-2-undecyl-3H-phenothiazin-3-one (23) as a red solid: yield 0.007 g (13%); silica gel TLC R_(f) 0.85 (ethyl acetate); ¹H NMR (CDCl₃) (500 MHz) S 0.87 (t, 3H, J=1 Hz), 1.26 (s, 18H), 1.70 (m, 2H), 2.70 (t, 2H, J=8 Hz), 2.86 (s, 5H), 6.72 (d, 1H, J=2 Hz), 6.88 (dd, 1H, J=2 Hz), 6.92 (s, 1H), 7.58 (d, 1H, J=9.5 Hz) and 7.70 (s, 1H); ¹³C NMR (CDCl₃) (125 MHz) δ 14.26, 22.84, 29.49, 29.63, 29.72, 29.80, 30.11, 31.64, 32.08, 44.01, 44.05, 112.82, 119.24, 119.27, 123.35, 133.97, 134.57, 135.47, 136.42, 139.75, 143.28, 155.84 and 182.45; mass spectrum (APCI), m/z (M+H)⁺411.2463 (C₂₅H₃₅N₂OS requires 411.2470); ultraviolet/visible spectrum λ_(max) 554.9 nm (in dichloromethane), λ_(max) 565.0 nm (in methanol).

Example 24

(1-decyl)triphenylphosphonium bromide (0.79 g, 1.64 mmol) was dissolved in anhydrous tetrahydrofuran. The reaction medium was cooled to −78° C. and sodium bis(trimethylsilyl) amide (1.64 ml (1.47 g), 1.64 mmol) was added dropwise. The reaction mixture was stirred at 0° C. for 3 h. Thereafter, the mixture was cooled to −78° C. and 2 (0.53 g, 1.64 mmol), pre-dissolved in anhydrous tetrahydrofuran was added. The reaction mixture was stirred at 0° C. for 18 h. The product was extracted with dichloromethane. The organic phase was washed with brine, dried (Na₂SO₄) and concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×1 cm). Elution with 4:1 hexane/dichloromethane afforded (E)-tert-butyl-2-(undec-1-enyl)-1 OH-phenothiazine-10-carboxylate (24) as a yellow solid: yield 0.14 g (20%); ³H NMR (CDCl₃) (400 MHz) δ 0.93 (t, 3H, J=6.4 Hz), 1.31 (s, 13H), 1.53 (s, 10H), 2.38 (q, 2H,J=7 Hz), 5.71 (m, 1H), 6.40 (d, 1H, J=11.2 Hz), 7.13 (m, 2H), 7.28 (q, 2H, J=7.4 Hz), 7.35 (d, 1H, J=7.6 Hz), 7.49 (s, 1H) and 7.57 (d, 1H, J=7.6 Hz); ¹³C NMR (CDCl₃) (100 MHz) δ 14.26, 22.84, 27.36, 28.32, 29.48, 29.73, 29.78, 29.93, 30.07, 32.07, 82.10, 126.14, 126.64, 127.36, 127.54, 127.81, 127.90, 129.99, 130.02, 130.06, 132.34, 134.01, 136.79, 138.65, 138.92 and 152.59; mass spectrum (APCI), m/z (M+H)⁺452.2617 (C₂₈H₃₈NO₂S requires 452.2623).

Example 25

24 (0.65 g, 1.45 mmol) was dissolved in anhydrous dichloromethane. Trifluoroacetic acid (0.88 ml (1.31 g), 11.60 mmol) was added dropwise. The reaction mixture was stirred at room temperature for 18 h. The product was mixed with sodium bicarbonate, extracted with dichloromethane, dried (Na₂SO₄) and then concentrated under diminished pressure. The residue was purified by chromatography on a silica gel column (20×1 cm). Elution with 9:1 hexane/ethyl acetate afforded (E)-2-(undec-1-enyl)-10H-phenothiazine (25) as a white solid: yield 0.21 g (100%).

Example 26

N-(7-(dimethylamino)-(E)-2-(undec-1-enyl)-3H-phenothiazin-3-ylidene)-N-methyl methanaminium iodide (26)

25 (0.45 g, 1.30 mmol) was dissolved in dichloromethane. Iodine (1.10 g, 4.10 mmol) was added and the reaction was run in the dark for 15 minutes. Thereafter, dimethylamine (3.30 ml (2.21 g), 6.50 mmol) was added dropwise and the reaction was allowed to run for 4 h. The product was dissolved in dichloromethane and the solution was concentrated under diminished pressure. The crude product N-(7-(dimethylamino)-(E)-2-(undec-1-enyl)-3H-phenothiazin-3-ylidene)-N-methyl methanaminium iodide (26) was obtained as a green solid. Mass spectrum (MALDI-TOF), m/z (M⁺) 436.696 (C₂₇H₃₈N₃S requires 436.2781).

Example 27

7-(dimethylamino)-(E)-2-(undec-1-enyl)-3H-phenothiazin-3-one (27)

26 (0.19 g, 0.43 mmol) was dissolved in a mixture of tetrahydrofuran/water (6:1). Solid KOH (0.025 g, 0.43 mmol) was added and the reaction mixture was stirred for 10 minutes when the colour changed from green to red. The reaction was quenched with water. The product was extracted in ethyl acetate, washed with brine, dried (Na₂SO₄) and was concentrated under diminished pressure. The crude product 7-(dimethylamino)-(E)-2-(undec-1-enyl)-3H-phenothiazin-3-one (27) was obtained as a red solid. Mass spectrum (MALDI-TOF), m/z (M⁺) 408.736 (C₂₅H₃₂N₂OS requires 408.2235).

Examples 28-32

Examples 28-32 shown below in Table 1, are prepared essentially according to the synthetic methodology described herein, and/or by using methodology well known in the art.

TABLE 1 Ex. No. Chemical Structure 28

29

30

31

32

Example 33

7-(butyl(pentadecyl)amino)-3H-phenothiazin-3-one (33)

2-(2,4-Dinitrophenyl)thio)-5-methoxyaniline (34): 2.00 g (11.1 mmol) of 2-amino-6-methoxybenzothiazole was suspended in 40 ml of water and 9.30 g (167 mmol) of solid KOH was added. The suspension was heated to reflux for 12 h. The reaction mixture was cooled to room temperature and added dropwise to a solution of 2.25 g (11.1 mmol) of 2, 4-dinitrochlorobenzene in a mixture of ethanol (30 mL) AcOH (20 mL) in ice water bath. The reaction mixture was stirred at room temperature for an additional 3 h. The precipitate was filtered, washed with water-ethanol (1:1, v/v) and dried to afford 34 as an orange solid: yield 2.90 g (81%); silica gel TLC A/0.7 (3:7 ethyl acetate-hexanes); ¹H NMR (CD₃COCD₃) δ 3.76 (s, 3H), 6.85 (d, 1H, J=8.8 Hz), 6.97 (d, 1H, J=2.8 Hz), 7.00-7.06 (m, 2H), 8.18 (dd, 1H, J=9.2 Hz, J=2.6 Hz) and 9.12 (d, 1H, J=2.4 Hz); ¹³C NMR (DMSO-d₆) δ 55.9, 111.0, 117.5, 120.4, 120.6, 121.6, 127.1, 128.6, 143.3, 144.4, 144.6, 145.8 and 153.0; mass spectrum (APCI), m/z 322.0499 (M+H)⁺ (C₁₃H₁₂N₃O₅S requires m/z 322.0498).

N-(2-((2, 4-Dinitrophenyl)thio)-5-methoxyphenyl)acetamide (35): To a solution of 2.90 g (9.03 mmol) of 34 in 10 mL of anhydrous DMF was added 3.66 mL (2.74 g, 27.1 mmol) of anhydrous triethylamine followed by 4.30 mL (4.64 g, 45.5 mmol) of acetic anhydride. The reaction mixture was stirred for 12 h at room temperature and quenched by pouring into ice-cold water. The aqueous layer was extracted with four 25-mL portions of ethyl acetate. The combined organic layer was dried over anhydrous MgSO₄, filtered and concentrated under diminished pressure. The residue was purified on a silica gel column (8×4 cm). Elution with 3:7 ethyl acetate-hexanes afforded 35 as a bright yellow solid: yield 2.95 g (90%); silica gel TLC R_(f)0.57 (3:7 ethyl acetate-hexanes); ¹H NMR (DMSO-d₆) δ 1.86 (s, 3H), 3.77 (s, 3H), 6.99 (d, 1H, J=8.8 Hz), 7.18 (dd, 1H, J=8.8 Hz, J=2.4 Hz), 7.23 (d, 1H, J=2.8 Hz), 7.66 (d, 1H, J=8.8 Hz), 8.32 (dd, 1H, J=9.0 Hz, J=2.6 Hz), 8.88 (d, 1H, J=2.4 Hz) and 9.43 (br s, 1H); ¹³C NMR (DMSO-d₆) δ 22.8, 55.6, 117.7, 120.5, 121.0, 123.8, 127.5, 128.1, 129.2, 133.7, 144.05, 144.07, 145.6, 157.2 and 168.7; mass spectrum (APCI), m/z 364.0609 (M+H)⁺ (C₁₅H₁₄N₃O₆S requires m/z 364.0603).

3-Methoxy-7-nitro-10H-phenothiazine (36): To a stirred solution of 2.95 g (8.13 mmol) of 35 in 20 mL of acetone, under reflux, was added 0.91 g (16.2 mmol) of KOH in portions. The reaction mixture was kept under reflux for an additional 3 h and poured into ice-cold water. The aqueous layer was extracted with four 25-mL portions of ethyl acetate. The combined organic layer was dried over anhydrous MgSO₄, filtered and concentrated under diminished pressure. The residue was purified on a silica gel column (8×2 cm). Elution with 1:1 ethyl acetate-hexanes gave 36 as a violet solid: yield 2.00 g (90%); silica gel TLC R_(f) 0.43 (3:7 ethyl acetate-hexanes); ³H NMR (CD₃COCD₃) S 3.70 (s, 3H), 6.57-6.70 (m, 4H), 7.73 (d, 1H, J=2.4 Hz), 7.81-7.84 (m, 1H) and 8.47 (br s, 1H); ¹³C NMR (CD₃COCD₃) δ 55.0, 111.7, 113.0, 113.3, 116.1, 117.0, 117.2, 121.6, 124.2, 132.4, 141.5, 148.3 and 156.6; mass spectrum (APCI), m/z 275.0488 (M+H)⁺ (C₁₃HnN₂O₃S requires m/z 275.0490).

tert-Butyl 3-Methoxy-7-nitro-10H-phenothiazin-10-carboxylate (37): To a solution of 1.42 g (5.18 mmol) of 36 in 20 mL of anhydrous DMF at 0° C. was added 0.55 g (13.7 mmol) of 60% NaH. The reaction mixture was stirred at 0° C. for another 15 mins and 2.40 g (11.0 mmol) of di-tert-butyl dicarbonate was added. The reaction mixture was stirred at room temperature for 4 h, and was quenched with 30 mL of water. The aqueous layer was extracted with three 20-mL portions of ethyl acetate. The combined organic layer was washed with 20 mL of brine, dried over anhydrous MgSO₄ and concentrated under diminished pressure. The residue was purified on a silica gel column (8×4 cm). Elution with 3:7 ethyl acetate hexanes afforded 37 as a bright yellow solid: yield 1.66 g (86%); silica gel TLC Ry 0.54 (3:7 ethyl acetate-hexanes); ¹H NMR (CD₃COCD₃) δ 1.54 (s, 9H), 3.86 (s, 3H), 6.97 (dd, 1H, J=9.2 Hz, J=2.8 Hz), 7.01 (d, 1H, J=2.8 Hz), 7.47 (d, 1H, J=9.2 Hz), 7.84 (d, 1H, 7=8.8 Hz), 8.20 (dd, 1H, J=9.0 Hz, J=2.6 Hz) and 8.24 (d, 1H, 7=2.4 Hz); ¹³CNMR (CD₃COCD₃) S 29.2, 57.1, 84.3, 113.3, 115.6, 123.7, 124.1, 129.8, 130.0, 132.3, 133.1, 135.3, 146.9, 147.1, 153.2 and 159.9; mass spectrum (APCI), m/z 374.0932 (M+H)^(+(C) ₁₈H₁₉N₂O₅S requires m/z 374.0936).

tert-Butyl 3-Amino-7-methoxy-10H-phenothiazin-10-carboxylate (38): To a suspension of 0.42 g (1.12 mmol) of 37 in 10 mL of ethanol was added 10 mg of 10% Pd on activated carbon. The reaction mixture was stirred at room temperature under hydrogen atmosphere (25 psi) overnight. The reaction mixture was filtered through a celite pad and concentrated under diminished pressure. The crude product (38) was used for the next reaction without further purification.

tert-Butyl 3-(Pentadecylamino)-7-methoxy-10H-phenothiazin-10-carboxylate (39): 2.11 g (7.25 mmol) of 1-bromopentadecane in 3 mL of acetonitrile was added into a mixture of 0.50 g (˜ 1.45 mmol) of crude compound 38 in 2 mL of acetonitrile and 1.55 g (14.6 mmol) of Na₂CO₃. The reaction mixture was sealed under nitrogen atmosphere and stirred at 80° C. for ˜ 3 days. The reaction mixture was cooled to room temperature and filtered. The filtrate was concentrated under diminished pressure and purified on a silica gel column. Elution with 1:9 ethyl acetate hexanes gave compound 39 as a pale yellow solid: yield 0.14 g (9%); silica gel TLC R_(f)0.31 (1:9 ethyl acetate-hexanes) ¹H NMR (CDCl₃) δ 0.87 (t, 3H, 7=6.6 Hz), 1.25 (br s, 24H), 1.45 (s, 9H), 1.52-1.57 (m, 2H), 3.04 (t, 2H, 7=7.2 Hz), 3.76 (s, 3H), 6.45 (dd, 1H, 7=8.6 Hz, 7=2.6 Hz), 6.50 (d, 1H, 7=2.8 Hz), 6.76 (dd, 1H, J=8.8 Hz, 7=2.8 Hz), 6.83 (d, 1H, 7=2.8 Hz), 7.24 (d, 1H, 7=8.4 Hz) and 7.36 (d, 1H, 7=8.8 Hz); ¹³C NMR (CDCl₃) S 14.2, 22.8, 27.2, 28.20, 28.27, 28.31, 28.4, 29.46, 29.5, 29.69, 29.70, 29.75, 29.8, 32.0, 44.2, 55.7, 81.4, 109.8, 111.65, 111.7, 112.8, 127.6, 127.8, 128.7, 132.5, 132.7, 133.3, 146.7, 153.3 and 157.3; mass spectrum (APCI), m/z 555.3629 (M+H)^(+(C) ₃₃H₅₁N₂O₃S requires m/z 555.3620).

tert-Butyl 3-(Butylpentadecylamino)-7-methoxy-10H-phenothiazin-10-carboxylate (40): 0.11 mL (0.14 g, 1.00 mmol) of 1-bromobutane was added into a mixture of 90.0 mg (0.16 mmol) of compound 39 in 2 mL of acetonitrile and 0.17 g (1.60 mmol) of Na₂CO₃. The reaction mixture was sealed under nitrogen atmosphere and stirred at 80° C. for ˜ 30 h. The reaction mixture was cooled to room temperature and filtered. The filtrate was concentrated under diminished pressure. The crude was used to the next step without further purification.

7-(Butylpentadecylamino)-3H-phenothiazin-3-one (33). 0.48 mL (0.48 mmol) of 1 M BBr₃ in CH₂Cl₂ was added dropwise into the solution of 100 mg (˜0.16 mmol) of crude compound 40 in 2 mL of CH₂Cl₂ at −78° C. The reaction mixture was stirred overnight at ambient temperature and was quenched with 10 mL of water. The product was extracted with two 10-mL portions of ethyl acetate. The combined organic layer was washed with 20 mL of brine, dried over anhydrous Na₂SO₄ and concentrated under reduced pressure. The resulting violet solid was purified on a silica gel column (7×2 cm). Elution with 3:7 ethyl acetate-hexanes afforded 33 as a violet solid: yield 20 mg (25%); silica gel TLC R_(f)0.50 (1:4 ethyl acetate-hexanes); ¹H NMR (CDCl₃) δ 0.88 (t, 3H, J=6.6 Hz), 1.00 (t, 3H, J=7.2 Hz), 1.26-1.43 (m, 26H), 1.62-1.64 (m, 4H), 3.36-3.41 (m, 4H), 6.55 (d, 1H, J=2.4 Hz), 6.71 (s, 1H), 6.79-6.85 (m, 2H), 7.57 (d, 1H, J=9.6 Hz) and 7.68 (d, 1H, J=9.2 Hz); ¹³C NMR (CDCl₃) S 14.3, 22.8, 27.1, 27.5, 29.50, 29.53, 29.6, 29.7, 29.77, 29.79, 29.81, 29.83, 32.1, 51.5, 104.8, 113.3, 118.7, 128.7, 131.0, 132.4, 134.9, 136.0, 139.6, 140.0, 150.0 and 182.4; mass spectrum (APCI), m/z 495.3330 (M+H)⁺ (C₃₁H₄₇N₂OS requires m/z 495.3331).

Biological Example 1: Biochemical and Biological Evaluation Cell Lines and Culture Conditions

Human mitochondrial disease cell line, Friedreich's ataxia lymphocytes (GM15850) was obtained from Coriell Cell Repositories (Camden, N.J.). Lymphocytes were cultured in RPMI-1640 medium (Gibco, Life Technologies, Grand Island, N.Y.) with 15% fetal calf serum, 2 mM glutamine (HyClone, South Logan, Utah) and 1% penicillin-streptomycin antibiotic supplement (Cellgro, Manassas, Va.). Cells were passaged every other day to maintain them in log phase growth and kept at a nominal concentration of 5-10×10⁵ cell/mL. A CoQ₁₀ deficient lymphocyte cell line (GM17932) was obtained from Coriell Cell Repositories. A nutrient sensitized screening strategy to identify methylene blue analogues that function within the mitochondrial respiratory chain was used by growing the CoQ₁₀-deficient or FRDA lymphocytes in galactose containing media to force energy production predominantly through oxidative phosphorylation rather than glycolysis.¹⁻⁴ The lymphocytes were cultured in RPMI 1640 glucose free medium (Gibco, Grand Island, N.Y.) supplemented with 25 mM galactose, 2 mM glutamine and 1% penicillin-streptomycin, and 10% dialyzed fetal bovine serum (FBS) (<0.5 μg/mL) (Gemini Bio-Product, West Sacramento, Calif.).

Cytotoxicity Assay

Evaluation of methylene blue analogues for their cytoxicity and their ability to function within the mitochondrial respiratory chain was carried out by incubation of the prepared compounds for 24 or 48 h with FRDA lymphocytes. We have used a nutrient-sensitized screening strategy by culturing FRDA cells in galactose as the sole sugar source which forces mammalian cells to rely on mitochondrial oxidative phosphorylation (OXPHOS) to produce their ATP; they also become more sensitive to mitochondrial respiratory chain inhibitors than cells grown in glucose medium. Methylene blue analogues were tested for their cytotoxicity in FRDA lymphocytes using a simultaneous staining with a two-color fluorescence assay, the Live/Dead® Viability/Cytotoxicity Kit (Molecular Probes). This assay is used to measure two recognized parameters of cell viability, intracellular esterase activity and plasma integrity. The membrane-impermeant DNA dye ethidium homodimer-1 (EthD-1) was used to identify dead cells whose plasma membrane integrity was disrupted. The membrane-permeant dye calcein-AM was used to label live cells. It penetrates into the cells where it is metabolized by cytoplasmic esterases and becomes a fluorescent but membrane-impermeant probe which is retained in viable cells. One mL of FRDA lymphocyte cells (5×10⁵ cells) was plated in a 24-well plate in glucose free media (galactose 25 mM), treated with the test compounds and incubated at 37° C. for 24 h or 48 h in a humidified atmosphere containing 5% CO₂ in air. Cells were collected by centrifugation at 300×g for 3 min and washed with phosphate buffered saline. Cells were resuspended in phosphate buffered saline containing 25 mM galactose. Cell suspension was stained with 0.1 μM calcein AM and 0.2 μM EthD-1 and incubated in the dark at 37° C. for 15 minutes. Cells were collected by centrifugation at 300×g for 3 min and then washed with PBS. The samples were analyzed immediately by flow cytometry (C6 Accuri, BD Biosciences, San Jose, Calif.), using a 488 nm excitation laser and the and the FL1-H channel 530 ±15 nm emission filter and the FL2-H channel 585 ±15 nm. For each analysis 10,000 events were recorded and analyzed using C6 Accuri software (BD Biosciences).

Suppression of Reactive Oxygen Species

The ability of the methylene blue analogues to suppress ROS induced by depletion of glutathione was evaluated in FRDA lymphocyte cells. The intracellular ROS level was measured based on the ROS-induced formation of the highly fluorescent product 2′,7′-dichlorofluorescein (DCF) from the non-fluorescent dye 2′,7′-dichlorodihydrofluorescein diacetate (DCFH-DA). Briefly, 1 mL of FRDA lymphocytes (5×10⁵ cells) was plated in a 24-well plate, treated with the test compounds and incubated at 37° C. for 16 h in a humidified atmosphere containing 5% CO₂ in air. Cells were treated with 5 mM diethyl maleate (DEM) for 80 min, collected by centrifugation at 300×g for 3 min and then washed with phosphate buffered saline (Life Technologies). Cells were resuspended in PBS containing 20 mM glucose and incubated at 37° C. in the dark for 25 min with 10 μM DCFH-DA. Cells were collected by centrifugation at 300×g for 3 min and then washed with PBS. The samples were analyzed immediately by flow cytometry (C6 Accuri, BD Biosciences, San Jose, Calif.), using a 488 nm excitation laser and the FL1-H channel 530 ±15 nm emission filter. The generation of ROS, mainly peroxides, was detected as a result of the oxidation of DCFH. In each analysis, 10,000 events were recorded after cell debris was electronically gated out. Results obtained were verified by running duplicates and repeating experiments in three independent runs. Results were expressed as a percentage of median fluorescent intensity relative to FRDA-treated control.

Preservation of mitochondrial membrane potential (Δψ_(m))

The ability of the test compounds to depolarize or maintains mitochondrial inner membrane potential (Δψ_(m)) was assessed using the JC-1 probe. JC-1 is a cationic dye which exhibits potential-dependent accumulation in mitochondria. JC-1 is a dual stain, which can identify high membrane potential through J-aggregates (red fluorescence) and low membrane potential through J-monomers (green fluorescence). When the Δψ_(m) collapses, the reagent (JC-1) no longer accumulates inside the mitochondria; instead, it is diffuses throughout the cell cytosol in the monomeric form which fluoresces green. The detection of mitochondrial depolarization using JC-1 was accomplished by flow cytometry as described before (Arce et al. (2012) Bioorg. Med Chem. 20, 5188). Briefly, FRDA lymphocytes cells (5×10⁵ cells) were pre-treated with or without the test compounds for 16 h. The cells were incubated at 37° C. in the dark for 20 min with 1 μM JC-1. Cells were collected by centrifugation at 300×g for 3 min and washed with phosphate buffered saline. Cells were resuspended in phosphate buffered saline supplemented with 20 mM glucose and were analyzed immediately by FACS (C6 Accuri, BD Biosciences, San Jose, Calif.), using a 488 nm excitation laser and the FL1-H channel 530 ±15 nm emission filter and the FL2-H channel 585 ±15 nm. For each analysis 10,000 events were recorded and analyzed using C6 Accuri software (BD Biosciences). FCCP (carbonyl cyanide p-trifluoromethoxyphenyl hydrazone), a mitochondrial uncouple, was used to produce a negative control.

Cellular ATP Levels

A nutrient-sensitized screening strategy to identify methylene blue analogues that function within the mitochondrial respiratory chain and augment ATP was used as described before (Khdour et al. (2013) ACS Med Chem. Lett. 4, 724). The intracellular ATP level was measured in glucose-free media. The cells were grown on galactose-containing media to maximize ATP production via oxidative phosphorylation, and they become more sensitive to mitochondrial respiratory chain inhibitors than cells grown on glucose medium. While we have not identified any of these compounds which reliably increase ATP levels in cultured cells, as we had found previously for pyrimidinol analogues, we did verify that none of the analogues being considered for further study significantly decreased ATP production, thereby avoiding mitochondrial toxins. Briefly FRDA lymphocytes (2×10⁵ cell/mL) were plated (1 mL in 24-well plates) in glucose-free media supplemented with galactose and treated with the test compounds at final concentrations of 250, 300, 2500 and 5000 nM, and then incubated at 37° C. for 24 h or 48 h in a humidified atmosphere containing 5% CO₂ in air. Wells were mixed and cells in each well were transferred (100 μL) to 96-well microtiter black-walled cell culture plates (Costar, Corning, N.Y.). The total intracellular ATP level was measured in a luminator (Clarity™ luminescence microplate reader) using an ATP Bioluminescence Assay Kit (ViaLight-Plus ATP monitoring reagent kit, Lonza, Walkersville, Md.) following the manufacturer's protocol. The total ATP level was expressed as a percentage of untreated control.

Cytoprotection

The cytoprotection conferred by the prepared compounds was determined in FRDA lymphocyte using a simultaneous staining with a two-color fluorescence assay, the Live/Dead® Viability/Cytotoxicity Kit (Molecular Probes). One mL of FRDA lymphocyte cells (5×10⁵ cells) was plated in a 24-well plate in glucose free media (galactose 25 mM), treated with the test compounds and incubated at 37° C. for 4 h. Cells were treated with 50 nM rotenone and incubated at 37° C. for 24 h or 48 h in a humidified atmosphere containing 5% CO₂ in air. Cells were collected by centrifugation at 300×g for 3 min and washed with phosphate buffered saline. Cells were resuspended in phosphate buffered saline containing 25 mM galactose. Cell suspension was stained with 0.1 μM calcein AM and 0.2 μM EthD-1 and incubated in the dark at 37° C. for 15 minutes. Cells were collected by centrifugation at 300×g for 3 min and then washed with PBS. The samples were analyzed immediately by flow cytometry (C6 Accuri, BD Biosciences, San Jose, Calif.), using a 488 nm excitation laser and the and the FL1-H channel 530 ±15 nm emission filter and the FL2-H channel 585 ±15 nm. For each analysis 10,000 events were recorded and analyzed using C6 Accuri software (BD Biosciences).

NADH Oxidase Activity

The effect of the methylene blue analogues on the activities of complexes I, III and IV within the respiratory chain was evaluated using bovine heart mitochondria during the oxidation of their respective substrate (NADH) as described previously. Briefly, a small scale preparation of bovine heart mitochondria was prepared as described before (Smith, A. L (1967), Methods Enzymol. 10, 81). Bovine heart submitochondrial particles (SMPs) were prepared as described by Matsuno-Yagi and stored in a buffer containing 0.25 M sucrose and 10 mM Tris-HCl, pH 7.4, at −80° C. (Matsuno-Yagi, A.; Hatefi, Y. J. (1985) J. Biol. Chem. 260, 11424). SMPs were diluted to 0.5 mg/mL. Mitochondrial complexes I, III, and IV activity were assayed at 30 C and monitored spectrophotometrically using a Beckman Coulter DU-530 (340 nm, ε=6.22 mM⁻¹ cm⁻¹). NADH oxidase activity was determined in 50 mM Hepes buffer containing 5 mM MgCl₂, pH 7.5, in a total volume of 2.5 mL. The final mitochondrial protein concentration was 30 μg/mL. The initial rates of NADH oxidation were calculated from the linear portion of the traces.

NADH: Ubiquinone Oxidoreductase Activity (Complex I Activity)

The inhibition of NADH-Q oxidoreductase activity was determined using the same experimental conditions described previously. SMPs (30 μg/mL) were incubated at 30° C. for 5 min with the test compound in 1 mL of 50 mM phosphate buffer, pH 7.4, containing 0.25 M sucrose, 1 mM MgCl₂, 2 μM antimycin A and 2 mM KCN. The reaction was initiated by the addition of 75 μM NADH and 15 μM coenzyme Ql. Enzymatic activity, measured by the decrease in NADH absorbance, was monitored at 340 nm.

In Vitro SIRT3 Deacetylation Activity

Further characterization the effects of the modified methylene blue analogue on mitochondrial bioenergetics and sirtuin activation is measured. The mitochondrial NAD⁺/NADH ratio is a critical factor in sirtuin activation. Thus, the modulation of the NAD⁺/NADH ratio appears to be a promising strategy to fix the impairment of mitochondrial respiration (hyperacetylation) found in FRDA as a result of Sirt3 inhibition. Complex I activity in bovine heart submitochondrial particles (SMP) was coupled with recombinant SIRT3 (rSIRT3) activity using a luminogenic acetylated sirt3 peptide substrate (Chemilum de Lys HDAC/SIRT Kit) and NADH. The co-substrate NAD⁺ was generated by oxidation of NADH in presence and absence of rotenone.

Frataxin Protein Expression (Western Blot)

Immortalized normal and FRDA lymphocyte cell lines were seeded at 500,000 cells per/mL (5 mL) in T-25 flask. Cultures were treated with the test compounds and incubated for 24 h. Cells were harvested by centrifugation, washed with saline buffer and then were lysed using 200 μL of lysis buffer (1% triton X-100, 0.1% SDS, Tris-HCl (50 Mm) pH 7.4, 150 mM NaCl, 0.5% sodium deoxycholate, 0.1 mM EDTA) with protease inhibitors (protease cocktail inhibitors (Roche Applied Science) and 1 mM phenylmethylsulfonyl fluoride (Sigma), and incubated on ice for 30 min with periodical mixing. These samples were cleared of insoluble material by centrifugation at 20,000×g for 10 min at 4° C. Total protein concentration was measured by the BCA kit (Thermo Fisher Scientific). NuPAGE LDS Sample Buffer (4×) and NuPAGE Reducing Agent (10×) was added the lysate and they were denatured at 95° C. for 5 min, then equal amounts of lysates (30 mg) were used for immunoblotting. Samples were resolved on a 4%-12% SDS-polyacrylamide Bis-Tris gels (Invitrogen) according to the manufacturer's recommendations and then proteins were transferred to nitrocellulose membranes. After blocking with Superblock-TBS (Thermo Fisher Scientific) for 1 hour to inhibit non-specific binding the blot was incubated with anti-frataxin monoclonal antibody (5 μg/mL) (18A5DB1) (Novex®) (Life technologies) overnight at 4° C. to detect endogenous frataxin in FRDA and normal lymphocytes. Following three 5-min washes with TBST, the blots were incubated with horseradish peroxidase-linked secondary anti-rabbit antibody IgGs (1:10,000, Sigma, in Superblock-TBS) at room temperature for 1 hr. The blots were washed three times for 5 min with TBST, rinsed with deionized H₂O, and developed with enhanced chemiluminescence (ECL) (BioRad Chemi-Doc) using West Pico Chemiluminescent Substrate (Pierce Biotechnology).

It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be incorporated within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated herein by reference for all purposes. 

1-107. (canceled)
 108. A method of treating or suppressing diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation, comprising administering to a subject in need of such treatment an effective amount a compound selected from the group consisting of:


109. The method of claim 108, wherein the compound is selected from the group consisting of:


110. The method of claim 108, wherein the compound is selected from the group consisting of:


111. The method of claim 108, wherein the compound is selected from the group consisting of:


112. The method of claim 108, wherein the compound is selected from the group consisting of:


113. The method of claim 108, wherein the compound is:


114. A method of treating or suppressing diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation, comprising administering to a subject in need of such treatment an effective amount a compound of formula:

wherein: Y is N⁺R⁴R⁵X or O; X⁻ is an inorganic or organic counterion selected from the group consisting of halide, hydroxide, nitrate, oxide, phosphate, sulfate, acetate, monofluoroacetate, difluoroacetate, trifluoroacetate, trimethylacetate, benzoate, 3-(4-hydroxybenzoyl)benzoate, 4-methylbicyclo[2.2.2]-oct-2-ene-1-carboxylate cinnamate, citrate, fumarate, glucoheptonate, gluconate, glutamate, glycolate, hexanoate, lactate, malate, maleate, malonate, mandelate, muconate, hydroxynaphthoate, oxalate, palmitate, propionate, 3-phenylpropionate, pyruvate, salicylate, stearate, succinate, lauryl sulfate, alkyl sulfonate, aryl sulfonate, and tartrate; (i) R¹ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, N(R⁷)₂, OR⁷, or SR⁷, wherein the C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, and C₂-C₂₀ alkynyl are each optionally substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of halogen, CN, NO₂, C₁-C₆ alkyl, C₁-C₆ haloalkyl, C(O)N(R⁸)₂, C(O)OR⁸, N(R⁸)₂, OR⁸, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, heterocyclyl, aryl, and heteroaryl, wherein each cycloalkyl, cycloalkenyl, heterocyclyl, aryl, and heteroaryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents; and R³ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, or OR⁷ wherein the C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, and C₂-C₂₀ alkynyl are each optionally substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of halogen, CN, NO₂, C₁-C₆ alkyl, C₁-C₆ haloalkyl, C(O)N(R⁸)₂, C(O)OR⁸, N(R⁸)₂, OR⁸, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, heterocyclyl, aryl, and heteroaryl, wherein each cycloalkyl, cycloalkenyl, heterocyclyl, aryl, and heteroaryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents; or (ii) R¹ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, N(R⁷)₂, OR⁷, or SR⁷, wherein the C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, and C₂-C₂₀ alkynyl are each optionally substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of halogen, CN, NO₂, C₁-C₆ alkyl, C₁-C₆ haloalkyl, C(O)N(R⁸)₂, C(O)OR⁸, N(R⁸)₂, OR⁸, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, heterocyclyl, aryl, and heteroaryl, wherein each cycloalkyl, cycloalkenyl, heterocyclyl, aryl, and heteroaryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents; and R³ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, or OR⁷, wherein the C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, and C₂-C₂₀ alkynyl are each optionally substituted with 1,2,3, or 4 substituents independently selected from the group consisting of halogen, CN, NO₂, C₁-C₆ alkyl, C₁-C₆ haloalkyl, C(O)N(R⁸)₂, C(O)OR⁸, N(R⁸)₂, OR⁸, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, heterocyclyl, aryl, and heteroaryl, wherein each cycloalkyl, cycloalkenyl, heterocyclyl, aryl, and heteroaryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents; R² is N(R¹²)₂; R⁴ and R⁵ together with the nitrogen atom to which they are attached, form a heterocyclyl, wherein the heterocyclyl is optionally substituted with 1 or more independently selected R⁹ substituents; R⁶ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, N(R¹¹)₂, OR¹⁰, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, heterocyclyl, aryl, or heteroaryl, wherein the C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, and C₂-C₂₀ alkynyl are each optionally substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of halogen, CN, NO₂, C₁-C₆ alkyl, Ct-Ce haloalkyl, CON(R⁸)₂, C(O)ORs, N(R⁸)₂, OR⁸, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, heterocyclyl, aryl, or heteroaryl, wherein each C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, heterocyclyl, aryl, and heteroaryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents; each R⁷ is independently hydrogen, C₁-C₆ alkyl, or C₁-C₆ haloalkyl; each R⁸ is independently hydrogen, C₁-C₆ alkyl, C₁-C₆ haloalkyl, C₃-C₈ cycloalkyl(C₁-C₆ alkyl), heterocyclyl(C₁-C₆ alkyl), aryl(C₁-C₆ alkyl), heteroaryl(C₁-C₆ alkyl), C₃-C₈ cycloalkyl, heterocyclyl, aryl, or heteroaryl, wherein each cycloalkyl, heterocyclyl, aryl, and heteroaryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents; each R⁹ is independently halogen, CN, N₃, NO₂, C₁-C₆ alkyl, C₁-C₆ haloalkyl, NH₂, NHC₁-C₆ alkyl, N(C₁-C₆ alkyl)₂, or OC₁-C₆ alkyl; R¹⁰ is C₁-C₆ alkyl, C₁-C₆ haloalkyl, C₃-C₈ cycloalkyl(C₁-C₆ alkyl), heterocyclyl(C₁-C₆ alkyl), aryl(C₁-C₆ alkyl), heteroaryl(C₁-C₆ alkyl), C₃-C₈ cycloalkyl, heterocyclyl, aryl, or heteroaryl, wherein the cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with 1 or more independently selected R⁹ substituents; each R¹¹ is independently hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl; and both R¹², together with the nitrogen atom to which they are attached, form a heterocyclyl, wherein the heterocyclyl is optionally substituted with 1 or more independently selected R⁹ substituents.
 115. The method of claim 114, wherein R¹ is C₁-C₂₀ alkyl, wherein the C₁-C₂₀ alkyl is optionally substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, and aryl, wherein each cycloalkyl, cycloalkenyl, and aryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents.
 116. The method of claim 114, wherein: R¹ is OR⁷; and R⁷ is C₁-C₆ alkyl.
 117. The method of claim 114, wherein R² is pyrrolidin-1-yl, piperidin-1-yl, azepan-1-yl, piperazin-1-yl, morpholin-4-yl, or diazepan-1-yl, each optionally substituted with 1 or more independently selected R⁹ substituents.
 118. The method of claim 114, wherein R³ is C₁-C₂₀ alkyl, C₁-C₂₀ alkenyl, C₁-C₂₀ alkynyl, or OR⁷, wherein the C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, and C₂-C₂₀ alkynyl are each optionally substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of halogen, CN, NO₂, C₁-C₆ alkyl, C₁-C₆ haloalkyl, C(O)N(R⁸)₂, C(O)OR⁸, N(R⁸)₂, OR⁸, C₃-C₈ cycloalkyl, C₃-C₅ cycloalkenyl, heterocyclyl, aryl, and heteroaryl, wherein each cycloalkyl, cycloalkenyl, heterocyclyl, aryl, and heteroaryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents.
 119. The method of claim 114, wherein R³ is C₅-C₂₀ alkyl, wherein the C₅-C₂₀ alkyl is optionally substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of OR⁸, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, and aryl, wherein each cycloalkyl, cycloalkenyl, and aryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents.
 120. The method of claim 114, wherein R³ is C₁-C₂₀ alkyl, wherein the C₁-C₂₀ alkyl is optionally-substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of OR⁸, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, and aryl, wherein each cycloalkyl, cycloalkenyl, and aryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents.
 121. The method of claim 114, wherein R³ is C₁₀-C₂₀ alkyl, wherein the C₁₀-C₂₀ alkyl is optionally substituted with 1, 2, 3, or 4 substituents independently selected from the group consisting of OR⁸, C₃-C₈ cycloalkyl, C₃-C₈ cycloalkenyl, and aryl, wherein each cycloalkyl, cycloalkenyl, and aryl is optionally and independently substituted with 1 or more independently selected R⁹ substituents.
 122. The method of claim 114, wherein R³ is heptadecyl.
 123. The method of claim 114, wherein R⁶ is hydrogen.
 124. The method of claim 114, wherein R⁶ is N(R¹¹)₂.
 125. The method of claim 114, wherein the compound selected from the group consisting of:


126. A method of treating or suppressing diseases associated with decreased mitochondrial function resulting in diminished ATP production and/or oxidative stress and/or lipid peroxidation, comprising administering to a subject in need of such treatment an effective amount a compound of formula:

wherein X⁻ is a counterion; R¹ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, —OR⁷, —SR⁷, —NHR⁷, or —N(R⁷)₂, each optionally substituted with one to four substituents selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, aryl, heteroaryl, and heterocycle, wherein each cycloalkyl, cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally substituted with one or more R⁹; where each R⁷ independently is hydrogen, C₁-C₆ alkyl, or halo(C₁-C₆ alkyl); where each R⁸ independently is hydrogen, C₁-C₆ alkyl, halo(C₁-C₆ alkyl), C₃-C₈ cycloalkyl, aryl, heteroaryl, heterocycle, aryl(C₁-C₆ alkyl), C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆ alkyl), heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆ alkyl), wherein each cycloalkyl, aryl, heteroaryl, and heterocycle are optionally substituted with one or more R⁹; where each R⁹ independently is halogen, —CN, —NO₂, —N₃, C₁-C₆ alkyl, halo(C₁-C₆ alkyl), C₁-C₆ alkoxy, amino, C₁-C₆alkylamino, or diC₁-C₆alkylamino; R² and R⁶ are independently —N(R¹¹)₂; where each R¹¹ independently is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl; R³ is hydrogen, C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, or —OR⁷, each optionally substituted with one to four substituents selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, aryl, heteroaryl, and heterocycle, wherein each cycloalkyl, cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally substituted with R⁹; R⁴ and R⁵ are independently C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl, each optionally substituted with one to four substituents selected from halogen, —CN, —NO₂, C₁-C₆ alkyl, halo(C₁-C₆ alkyl), —OR⁸, —NR⁸ ₂, —CO₂R⁸, —CONR⁸ ₂, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, aryl, heteroaryl, and heterocycle, wherein each cycloalkyl, cycloalkenyl, aryl, heteroaryl, and heterocycle are optionally substituted with R⁹; where R¹⁰ is C₁-C₆ alkyl, halo(C₁-C₆ alkyl), C₃-C₈ cycloalkyl, aryl, heteroaryl, heterocycle, aryl(C₁-C₆ alkyl), C₃-C₈cycloalkyl(C₁-C₆ alkyl), aryl(C₁-C₆ alkyl), heteroaryl(C₁-C₆ alkyl), or heterocycle(C₁-C₆ alkyl), wherein each cycloalkyl, aryl, heteroaryl, and heterocycle are optionally substituted with R⁹; and R⁷ is hydrogen or —N(R¹¹)₂.
 127. The method of claim 126, wherein R¹ is hydrogen, optionally substituted C₁-C₂₀ alkyl, optionally substituted C₂-C₂₀ alkenyl, optionally substituted C₂-C₂₀ alkynyl, or —OR⁷.
 128. The method of claim 126, wherein R² is —N(R¹¹)₂, where each R¹¹ independently is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl.
 129. The method of claim 126, wherein R² is —N(CH₃)₂.
 130. The method of claim 126, wherein R³ is hydrogen, optionally substituted C₁-C₂₀ alkyl, or —OR⁷.
 131. The method of claim 126, wherein R³ is C₅-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹.
 132. The method of claim 126, wherein R³ is C₇-C₂₀ alkyl optionally substituted with —OR⁸, C₃-C₈ cycloalkyl, C₃-C₈cycloalkenyl, or aryl, wherein each cycloalkyl, cycloalkenyl, and aryl are optionally substituted with R⁹.
 133. The method of claim 126, wherein R³ is heptadecyl.
 134. The method of claim 126, wherein R⁷ is hydrogen.
 135. The method of claim 126, wherein R⁷ is —N(CH₃)₂.
 136. The method of claim 126, wherein the compound is:


137. The method of claim 108, wherein the disease is selected from the group consisting of Friedreich's ataxia, Leber's Hereditary Optic Neuropathy, Kearns-Sayre Syndrome, Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-Like Episodes, Leigh syndrome, amyotrophic lateral sclerosis, Huntington's disease, Alzheimer's disease and Parkinson's disease.
 138. The method of claim 114, wherein the disease is selected from the group consisting of Friedreich's ataxia, Leber's Hereditary Optic Neuropathy, Kearns-Sayre Syndrome, Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-Like Episodes, Leigh syndrome, amyotrophic lateral sclerosis, Huntington's disease, Alzheimer's disease and Parkinson's disease.
 139. The method of claim 126, wherein the disease is selected from the group consisting of Friedreich's ataxia, Leber's Hereditary Optic Neuropathy, Kearns-Sayre Syndrome, Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-Like Episodes, Leigh syndrome, amyotrophic lateral sclerosis, Huntington's disease, Alzheimer's disease and Parkinson's disease.
 140. A method for treating or protecting mitochondria with respiratory chain lesions, comprising administering to a subject in need of such treatment an effective amount of one or more compounds according to claim
 108. 141. A method for treating or protecting mitochondria with respiratory chain lesions, comprising administering to a subject in need of such treatment an effective amount of one or more compounds according to claim
 114. 142. A method for treating or protecting mitochondria with respiratory chain lesions, comprising administering to a subject in need of such treatment an effective amount of one or more compounds according to claim
 126. 